question #684
Replies: 16 comments 8 replies
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Please share some information on what you want to do to make it easier for people to answer your question. Regarding Orca, you need an installation of Depending on your platform, installation instructions differ slightly. Without this information I cannot answer this question other than by referring you to https://xtb-docs.readthedocs.io/en/latest/setup.html for the general instructions. |
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Thank you so much. I want to calculate pKa of some flexible molecules, which have carboxylic functional group. I have a problem to find low-energy conformers to find reliable and agreement pKa respect to experimental data. by changing the initial conformer, i had different conformer. Until i found Dr Grimme's paper, attached paper, Thank you so much |
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I am waiting for your answer. Could you please answer me? Could you please help me in installing CREST package? Thank you so much |
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I have been on vacation until today, please be patient. Also, please consider that many of us are working beside our research or on volunteer basis on this project. I'm happy to help out whenever I can, however this will only work efficiently for both of us if you provide more information on the platform / machine / computer you are using. |
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Since I don't know what platform you are working on, I can only share some general comments with you, which should work for Linux and MacOS.
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Dear Sebastian Ehlert
Thank you so much for your encouraged response and I apologize for my
hurried behaviour.
Linux has not been installed in my system and now I am going to install it.
In your opinion, with below specification of my system, half of the space
is sufficient for installing Linux OR should I install linux with all of my
system space? I mentioned that I am going to install ORCA+xtb+CREST on
Linux. How do I divide my space until in calculation progress, I don't face
inefficient space or memory error?
my specification system is listed below:
Processor(CPU):core i7-6700k cpu @ 4.00 GHZ 4.00 GHZ
Installed memory: 32.0 GB
system type:64bit operating system
I have one driver and its space Drive C: 476 GB
Thank you so much
With Regards
…On Mon, Sep 5, 2022 at 4:53 PM Sebastian Ehlert ***@***.***> wrote:
Since I don't know what platform you are working on, I can only share some
general comments with you, which should work for Linux and MacOS.
1. Install mambaforge
<https://github.com/conda-forge/miniforge#mambaforge> for Linux/x86_64
this works by running the following commands in your terminal (the
installer is interactive)
wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh -O Mambaforge.sh
sh Mambaforge.sh
1. Restart the terminal
exec $SHELL
1. Create an environment for xtb and crest (make sure to pin libblas
to MKL for optimal performance on x86_64 machines)
mamba create -n crest crest xtb 'libblas=*=*mkl*'
1. Activate the environment and check whether xtb and crest are
available
mamba activate crest
xtb --version
crest --version
1. Create otool_xtb to register xtb with Orca
ln -s $(command -v xtb) ${$(command -v orca_scf)/orca_scf/otool_xtb}
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While you still haven't told me yet, I presume you are on a Windows machine (drive C is a giveaway). This information would have been useful in the initial question. You can use ORCA and xtb on Windows, however CREST does not support this platform. An option is to use Windows Subsystem Linux (WSL) and install the required programs there, you can find the instructions we give to our master students for this at https://qc2-teaching.readthedocs.io/en/latest/install.html#install-wsl, then you can follow the steps shown above. Also, I cannot give you any advice on how to setup or repartition you computer, that's something you have to learn on your own or ask in a forum which usually deals with this kind of questions. The same holds for any questions regarding the WSL setup, please look into the support provided by your operating system provider. |
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Thank you
yes, Windows 10 has been installed on my system.
With Regards
…On Thu, Sep 29, 2022 at 9:17 PM Sebastian Ehlert ***@***.***> wrote:
While you still haven't told me yet, I presume you are on a Windows
machine (drive C is a giveaway). This information would have been useful in
the initial question. You use ORCA and xtb on Windows, however CREST does
not support this platform. An option is to use Windows Subsystem Linux
(WSL) and install the required programs there, you can find the
instructions we give to our master students for this at
https://qc2-teaching.readthedocs.io/en/latest/install.html#install-wsl,
than you can follow the steps shown above.
Also, I cannot give you any advice on how to setup or repartition you
computer, that's something you have to learn on your own or ask a forum
which usually deals with this kind of questions. The same holds for any
questions regarding the WSL setup, please look into the support provided by
your operating system provider.
—
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<#684 (reply in thread)>,
or unsubscribe
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Dear Sebastian Ehlert
yesterday, I installed linuxmint20.2 on my system, although your link
suggested Ubuntu. Have it any problems during installing and working with
CREST and xtb?
Thank you so much
With Regards
On Thu, Sep 29, 2022 at 10:13 PM elham sookhaki ***@***.***>
wrote:
… Thank you
yes, Windows 10 has been installed on my system.
With Regards
On Thu, Sep 29, 2022 at 9:17 PM Sebastian Ehlert ***@***.***>
wrote:
> While you still haven't told me yet, I presume you are on a Windows
> machine (drive C is a giveaway). This information would have been useful in
> the initial question. You use ORCA and xtb on Windows, however CREST does
> not support this platform. An option is to use Windows Subsystem Linux
> (WSL) and install the required programs there, you can find the
> instructions we give to our master students for this at
> https://qc2-teaching.readthedocs.io/en/latest/install.html#install-wsl,
> than you can follow the steps shown above.
>
> Also, I cannot give you any advice on how to setup or repartition you
> computer, that's something you have to learn on your own or ask a forum
> which usually deals with this kind of questions. The same holds for any
> questions regarding the WSL setup, please look into the support provided by
> your operating system provider.
>
> —
> Reply to this email directly, view it on GitHub
> <#684 (reply in thread)>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/A2ZKRWIFBAZ3XT5S4GOPFG3WAXI2DANCNFSM6AAAAAAQAHNHVU>
> .
> You are receiving this because you authored the thread.Message ID:
> ***@***.***>
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If you have a specific installation question, there is the possibility to get an answer. For this general question I recommend to just try installing it and see for yourself whether the programs work. |
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Exactly, Linuxmint-20.2-cinnamon-64bit
Thank you so much
…On Sat, Oct 1, 2022 at 10:03 AM elham sookhaki ***@***.***> wrote:
Dear Sebastian Ehlert
yesterday, I installed linuxmint20.2 on my system, although your link
suggested Ubuntu. Have it any problems during installing and working with
CREST and xtb?
Thank you so much
With Regards
On Thu, Sep 29, 2022 at 10:13 PM elham sookhaki ***@***.***>
wrote:
> Thank you
> yes, Windows 10 has been installed on my system.
>
> With Regards
>
> On Thu, Sep 29, 2022 at 9:17 PM Sebastian Ehlert <
> ***@***.***> wrote:
>
>> While you still haven't told me yet, I presume you are on a Windows
>> machine (drive C is a giveaway). This information would have been useful in
>> the initial question. You use ORCA and xtb on Windows, however CREST does
>> not support this platform. An option is to use Windows Subsystem Linux
>> (WSL) and install the required programs there, you can find the
>> instructions we give to our master students for this at
>> https://qc2-teaching.readthedocs.io/en/latest/install.html#install-wsl,
>> than you can follow the steps shown above.
>>
>> Also, I cannot give you any advice on how to setup or repartition you
>> computer, that's something you have to learn on your own or ask a forum
>> which usually deals with this kind of questions. The same holds for any
>> questions regarding the WSL setup, please look into the support provided by
>> your operating system provider.
>>
>> —
>> Reply to this email directly, view it on GitHub
>> <#684 (reply in thread)>,
>> or unsubscribe
>> <https://github.com/notifications/unsubscribe-auth/A2ZKRWIFBAZ3XT5S4GOPFG3WAXI2DANCNFSM6AAAAAAQAHNHVU>
>> .
>> You are receiving this because you authored the thread.Message ID:
>> ***@***.***>
>>
>
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Dear friend,
Could you please tell me, does CREST have any restriction on number of
atoms in molecule or xtb in preoptimization? my molecule has 97 C, H and 4
N, and 8 O, named spiro-OMeTAD.
Thank you so much
With Regards
…On Sat, Oct 1, 2022 at 10:30 AM Sebastian Ehlert ***@***.***> wrote:
If you have a specific installation question, there is the possibility to
get an answer. For this general question I recommend to just try installing
it and see for yourself whether the programs work.
—
Reply to this email directly, view it on GitHub
<#684 (reply in thread)>,
or unsubscribe
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There are generally no atom restrictions in xtb nor in crest. Please check the setup page of xtb for possible causes. I would assume that you need to add |
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Could you please tell me what do i do when i write this commend an give bellow error? Command 'mamba' not found, did you mean: command 'samba' from deb samba (2:4.13.17~dfsg-0ubuntu1.20.04.1) Try: sudo apt install |
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Please install mamba following the instructions in |
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thank you so much |
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Sorry, copied the wrong link. The mamba installer can be found at https://github.com/conda-forge/miniforge |
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Dear Friend,
the address of mamba installer is identical to the below command in the
terminal (actually download mamba):
wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
-O Mambaforge.sh
am i right?
then I do this command:sh Mambaforge.sh
and perform it, in last line of licence agreement has been written
redistribution and use in source and binary forms, with or without. i
used control C.
mamba create -n crest crest xtb 'libblas=*=*mkl*' was performed in
terminal but again was written : command "mamba" not found.
i mention that i add addulimit -s unlimited to my .bashrc/.zshrc and
did again bove command but again was not found mamba.
Could you please help me?
Thank you so much
Regards
…On Sun, Nov 27, 2022 at 1:56 PM Sebastian Ehlert ***@***.***> wrote:
Sorry, copied the wrong link. The mamba installer can be found at
https://github.com/conda-forge/miniforge
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<#684 (reply in thread)>,
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Excuse me, should be used 'enter' instead of 'contl+C.
the answer of "do you wish the installer to initialize mambforg by running
condo inite" is yes or no? i don't know.
Thank you so much
Regards
…On Mon, Nov 28, 2022 at 1:25 PM elham sookhaki ***@***.***> wrote:
Dear Friend,
the address of mamba installer is identical to the below command in the
terminal (actually download mamba):
wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh -O Mambaforge.sh
am i right?
then I do this command:sh Mambaforge.sh
and perform it, in last line of licence agreement has been written redistribution and use in source and binary forms, with or without. i used control C.
mamba create -n crest crest xtb 'libblas=*=*mkl*' was performed in terminal but again was written : command "mamba" not found.
i mention that i add addulimit -s unlimited to my .bashrc/.zshrc and did again bove command but again was not found mamba.
Could you please help me?
Thank you so much
Regards
On Sun, Nov 27, 2022 at 1:56 PM Sebastian Ehlert ***@***.***>
wrote:
> Sorry, copied the wrong link. The mamba installer can be found at
> https://github.com/conda-forge/miniforge
>
> —
> Reply to this email directly, view it on GitHub
> <#684 (reply in thread)>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/A2ZKRWLXH5HHD2WUFYULDCDWKMZMFANCNFSM6AAAAAAQAHNHVU>
> .
> You are receiving this because you authored the thread.Message ID:
> ***@***.***>
>
|
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I choose yes. after install mambe this error was appeared. Could you please
help me?
An unexpected error has occurred. Conda has prepared the above report.
(base) ***@***.***:~$ mamba activate crest
EnvironmentNameNotFound: Could not find conda environment: crest
You can list all discoverable environments with `conda info --envs`.
(base) ***@***.***:~$ xtb --version
Command 'xtb' not found, did you mean:
command 'jtb' from deb jtb (1.4.12-2)
command 'xte' from deb xautomation (1.09-2)
command 'xtv' from deb xtv (1.1-15)
command 'xcb' from deb xcb (2.4-5)
Try: sudo apt install <deb name>
(base) ***@***.***:~$ crest --version
Command 'crest' not found, did you mean:
command 'mrest' from deb libweb-mrest-perl (0.288-1)
command 'ctest' from deb cmake (3.16.3-1ubuntu1.20.04.1)
Try: sudo apt install <deb name>
…On Mon, Nov 28, 2022 at 4:23 PM elham sookhaki ***@***.***> wrote:
Excuse me, should be used 'enter' instead of 'contl+C.
the answer of "do you wish the installer to initialize mambforg by running
condo inite" is yes or no? i don't know.
Thank you so much
Regards
On Mon, Nov 28, 2022 at 1:25 PM elham sookhaki ***@***.***>
wrote:
> Dear Friend,
>
> the address of mamba installer is identical to the below command in the
> terminal (actually download mamba):
>
> wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh -O Mambaforge.sh
> am i right?
>
> then I do this command:sh Mambaforge.sh
>
> and perform it, in last line of licence agreement has been written redistribution and use in source and binary forms, with or without. i used control C.
>
> mamba create -n crest crest xtb 'libblas=*=*mkl*' was performed in terminal but again was written : command "mamba" not found.
>
> i mention that i add addulimit -s unlimited to my .bashrc/.zshrc and did again bove command but again was not found mamba.
>
> Could you please help me?
>
> Thank you so much
>
> Regards
>
>
> On Sun, Nov 27, 2022 at 1:56 PM Sebastian Ehlert <
> ***@***.***> wrote:
>
>> Sorry, copied the wrong link. The mamba installer can be found at
>> https://github.com/conda-forge/miniforge
>>
>> —
>> Reply to this email directly, view it on GitHub
>> <#684 (reply in thread)>,
>> or unsubscribe
>> <https://github.com/notifications/unsubscribe-auth/A2ZKRWLXH5HHD2WUFYULDCDWKMZMFANCNFSM6AAAAAAQAHNHVU>
>> .
>> You are receiving this because you authored the thread.Message ID:
>> ***@***.***>
>>
>
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exactly, I take this error: please guide me. thank you so much
(base) ***@***.***:~$ mamba create -n crest crest xtb 'libblas=*=*mkl*'
…__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/
/██/
/████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗
███╗██████╗ █████╗
████╗ ████║██╔╠â•
██╗████╗ ████║██╔╠╠██╗██╔â•
╠██╗
██╔████╔██║███████║██╔████╔██║██████╔â•
███████║
██║╚██╔╠██║██╔╠â•
██║██║╚██╔╠██║██╔╠â•
██╗██╔╠╠██║
██║ ╚╠╠██║██║ ██║██║ â•šâ• â•
██║██████╔╠██║ ██║
â•šâ• â• â•šâ• â• â•šâ• â• â•šâ• â• â•šâ• â• â•šâ• â•
â•šâ• â• â• â• â• â• â•šâ• â• â•šâ• â•
mamba (1.0.0) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['crest', 'xtb', 'libblas=[build=*mkl*]']
conda-forge/linux-64 ??.?MB @ ??.?MB/s 0
failed 10.2s
Download error (28) Timeout was reached [
https://conda.anaconda.org/conda-forge/noarch/repodata.json]
Connection time-out
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File
"/home/elham/mambaforge/lib/python3.10/site-packages/conda/exceptions.py",
line 1129, in __call__
return func(*args, **kwargs)
File
"/home/elham/mambaforge/lib/python3.10/site-packages/mamba/mamba.py", line
935, in exception_converter
raise e
File
"/home/elham/mambaforge/lib/python3.10/site-packages/mamba/mamba.py", line
928, in exception_converter
exit_code = _wrapped_main(*args, **kwargs)
File
"/home/elham/mambaforge/lib/python3.10/site-packages/mamba/mamba.py", line
886, in _wrapped_main
result = do_call(parsed_args, p)
File
"/home/elham/mambaforge/lib/python3.10/site-packages/mamba/mamba.py", line
754, in do_call
exit_code = create(args, parser)
File
"/home/elham/mambaforge/lib/python3.10/site-packages/mamba/mamba.py", line
630, in create
return install(args, parser, "create")
File
"/home/elham/mambaforge/lib/python3.10/site-packages/mamba/mamba.py", line
497, in install
index = load_channels(pool, channels, repos)
File
"/home/elham/mambaforge/lib/python3.10/site-packages/mamba/utils.py", line
129, in load_channels
index = get_index(
File
"/home/elham/mambaforge/lib/python3.10/site-packages/mamba/utils.py", line
110, in get_index
is_downloaded = dlist.download(api.MAMBA_DOWNLOAD_FAILFAST)
RuntimeError: Download error (28) Timeout was reached [
https://conda.anaconda.org/conda-forge/noarch/repodata.json]
Connection time-out
`$ /home/elham/mambaforge/bin/mamba create -n crest crest xtb
libblas=*=*mkl*`
environment variables:
CIO_TEST=<not set>
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/elham/mambaforge/bin/conda
CONDA_PREFIX=/home/elham/mambaforge
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/home/elham/mambaforge/bin/python
CONDA_ROOT=/home/elham/mambaforge
CONDA_SHLVL=1
CURL_CA_BUNDLE=<not set>
PATH=/home/elham/mambaforge/bin:/home/elham/mambaforge/condabin:/usr/local/
sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/loca
l/games:/snap/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session0
active environment : base
active env location : /home/elham/mambaforge
shell level : 1
user config file : /home/elham/.condarc
populated config files : /home/elham/mambaforge/.condarc
conda version : 22.9.0
conda-build version : not installed
python version : 3.10.6.final.0
virtual packages : __linux=5.4.0=0
__glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/elham/mambaforge (writable)
conda av data dir : /home/elham/mambaforge/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /home/elham/mambaforge/pkgs
/home/elham/.conda/pkgs
envs directories : /home/elham/mambaforge/envs
/home/elham/.conda/envs
platform : linux-64
user-agent : conda/22.9.0 requests/2.28.1 CPython/3.10.6
Linux/5.4.0-74-generic linuxmint/20.2 glibc/2.31
UID:GID : 1000:1000
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
On Mon, Nov 28, 2022 at 5:02 PM elham sookhaki ***@***.***> wrote:
I choose yes. after install mambe this error was appeared. Could you
please help me?
An unexpected error has occurred. Conda has prepared the above report.
(base) ***@***.***:~$ mamba activate crest
EnvironmentNameNotFound: Could not find conda environment: crest
You can list all discoverable environments with `conda info --envs`.
(base) ***@***.***:~$ xtb --version
Command 'xtb' not found, did you mean:
command 'jtb' from deb jtb (1.4.12-2)
command 'xte' from deb xautomation (1.09-2)
command 'xtv' from deb xtv (1.1-15)
command 'xcb' from deb xcb (2.4-5)
Try: sudo apt install <deb name>
(base) ***@***.***:~$ crest --version
Command 'crest' not found, did you mean:
command 'mrest' from deb libweb-mrest-perl (0.288-1)
command 'ctest' from deb cmake (3.16.3-1ubuntu1.20.04.1)
Try: sudo apt install <deb name>
On Mon, Nov 28, 2022 at 4:23 PM elham sookhaki ***@***.***>
wrote:
> Excuse me, should be used 'enter' instead of 'contl+C.
> the answer of "do you wish the installer to initialize mambforg by
> running condo inite" is yes or no? i don't know.
>
> Thank you so much
> Regards
>
> On Mon, Nov 28, 2022 at 1:25 PM elham sookhaki ***@***.***>
> wrote:
>
>> Dear Friend,
>>
>> the address of mamba installer is identical to the below command in the
>> terminal (actually download mamba):
>>
>> wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh -O Mambaforge.sh
>> am i right?
>>
>> then I do this command:sh Mambaforge.sh
>>
>> and perform it, in last line of licence agreement has been written redistribution and use in source and binary forms, with or without. i used control C.
>>
>> mamba create -n crest crest xtb 'libblas=*=*mkl*' was performed in terminal but again was written : command "mamba" not found.
>>
>> i mention that i add addulimit -s unlimited to my .bashrc/.zshrc and did again bove command but again was not found mamba.
>>
>> Could you please help me?
>>
>> Thank you so much
>>
>> Regards
>>
>>
>> On Sun, Nov 27, 2022 at 1:56 PM Sebastian Ehlert <
>> ***@***.***> wrote:
>>
>>> Sorry, copied the wrong link. The mamba installer can be found at
>>> https://github.com/conda-forge/miniforge
>>>
>>> —
>>> Reply to this email directly, view it on GitHub
>>> <#684 (reply in thread)>,
>>> or unsubscribe
>>> <https://github.com/notifications/unsubscribe-auth/A2ZKRWLXH5HHD2WUFYULDCDWKMZMFANCNFSM6AAAAAAQAHNHVU>
>>> .
>>> You are receiving this because you authored the thread.Message ID:
>>> ***@***.***>
>>>
>>
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Sorry, while I'd like to help you, it seems like you are stuck with some more basic installation issues and we are not actually making progress here. You cannot expect anyone here to make sense of terminal output you copy and paste in this thread. Please, take some time to carefully review and understand the steps you are doing before continuing this discussion. Also, please don't take offense if me or others prioritize their time on other issues and don't answer your inquiries. We are all just volunteering our time here. |
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Dear friend,
Can CREST find the lowest energies of A(+)B(-) complex and dimer molecules?
unfortunately, I can't find these procedures in the CREST site. Could you
please guide me?
for calculating solvation energy in SMD or C-PCM, optimization with
implicit solvent models such as ALPB in XTB and CREST is necessary? because
with and without initial optimization with ALPB have different energies.
Thank you so much
With Regards
…On Mon, Nov 28, 2022 at 8:23 PM Sebastian Ehlert ***@***.***> wrote:
Sorry, while I'd like to help you, it seems like you are stuck with some
more basic installation issues and we are not actually making progress here.
You cannot expect anyone here to make sense of terminal output you copy
and paste in this thread. Please, take some time to carefully review and
understand the steps you are doing before continuing this discussion.
Also, please don't take offense if me or others prioritize their time on
other issues and don't answer your inquiries. We are all just volunteering
our time here.
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Dear friends, I worked and installed ORCA version 5.0.2. Is it necessary to install xtb? can i use CREST without installing xtb?
With Regards
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