Re: [AMBER] Question about MCPB.py tutorial with GAMESS-US

From: Li, Zhen via AMBER <amber.ambermd.org>
Date: Wed, 23 Oct 2024 20:03:09 +0000

Hi Felipe,

Glad it worked for one more step!

For the ion charge issue, again, MCPY.py is designed to model metal ions with protein residues (but still compatible with non-covalent ligands, which is CO3 in your case, as long as you provide mol2 and frcmod files for CO3).

Therefore, it is not suggested to consider CaCO3 as a “whole” ion with a charge of zero. It is still better to regard Ca2+ as a metal ion with a charge of 2 and then CO3 as a ligand with a charge of -2.

Suppose the error is still there. Please feel free to share your directory (or part of it that is giving errors) via Google Drive or Box. I can take a look.

Best regards,
Zhen.

From: Silva Carvalho, Felipe <felipe.silva-carvalho.csun.edu>
Date: Wednesday, October 23, 2024 at 1:46 PM
To: Li, Zhen <lizhen6.chemistry.msu.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: Question about MCPB.py tutorial with GAMESS-US
Hi Zhen,

Thank you very much for your help! That worked, but I am getting another error for the third step. It says:

"Error: the charges and atom numbers are mismatch for the standard model!"

I saw in the Q&A page that may be due to a couple of reasons, but since I am not using gaussian I was only left with "Such a kind of error may be because you added/deleted atoms in the Merz-Kollman analysis of the large model". However, I did not change anything on the large model files. Do you know what may be happening? I can provide my files if needed.

Another question I have is about my system's charge in the MCPB generated files. I am doing just a simple example: CaCO_3, with Ca^{2+} close enough to form a bond with CO_3^{2-}. This system has a net charge of zero, but in the input files for running GAMESS-US it has "ICHARG=2" (which is the charge of the calcium ion). My guess is that I could just set the charges to zero and proceed with the calculations. Is that correct?

Sincerely,
Felipe
________________________________
De: Li, Zhen <lizhen6.chemistry.msu.edu>
Enviado: quarta-feira, 23 de outubro de 2024 07:51
Para: Silva Carvalho, Felipe <felipe.silva-carvalho.csun.edu>; AMBER Mailing List <amber.ambermd.org>
Assunto: Re: Question about MCPB.py tutorial with GAMESS-US


Hi Felipe,



Here is the better solution. Turns out you need to specify “software_version gms” in your caco3.in<https://urldefense.proofpoint.com/v2/url?u=http-3A__caco3.in&d=DwQGaQ&c=Oo8bPJf7k7r_cPTz1JF7vEiFxvFRfQtp-j14fFwh71U&r=NgCylDEQBE0axDv2CZqG8l4J7GJcRRTGkieutsHMLXQ&m=EMp4riidrcIh5KcbPrtmPEZo_bDyz9JjWBjXqG5WcPLLMDn9rKfh__-La70kpOJa&s=HuGLW8IrOKGoZzLcvGK6Fs6n9Nnd_dEYmmATwa74MiM&e=> file. Otherwise, the code will, by default, look for Gaussian outputs. Hope it helps. You may also find GAMESS example files here: $AMBERHOME/AmberTools/test/pymsmt/mcpb/gms-ff14SB/.



Best regards,

Zhen.



From: Silva Carvalho, Felipe via AMBER <amber.ambermd.org>
Date: Tuesday, October 22, 2024 at 11:46 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] Question about MCPB.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__MCPB.py&d=DwQGaQ&c=Oo8bPJf7k7r_cPTz1JF7vEiFxvFRfQtp-j14fFwh71U&r=NgCylDEQBE0axDv2CZqG8l4J7GJcRRTGkieutsHMLXQ&m=EMp4riidrcIh5KcbPrtmPEZo_bDyz9JjWBjXqG5WcPLLMDn9rKfh__-La70kpOJa&s=RwUaHkOgk5QCDQ2-41T6HUT4qZY2zGTr5jH-MB-s8-c&e=> tutorial with GAMESS-US

Hello everyone,

I am going through the tutorial for MCPB.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__MCPB.py&d=DwQGaQ&c=Oo8bPJf7k7r_cPTz1JF7vEiFxvFRfQtp-j14fFwh71U&r=NgCylDEQBE0axDv2CZqG8l4J7GJcRRTGkieutsHMLXQ&m=EMp4riidrcIh5KcbPrtmPEZo_bDyz9JjWBjXqG5WcPLLMDn9rKfh__-La70kpOJa&s=RwUaHkOgk5QCDQ2-41T6HUT4qZY2zGTr5jH-MB-s8-c&e=> using my own system as a test. Since I do not have a gaussian license, I am running the QM calculations with GAMESS-US. However, after getting the log files, it is not clear to me how to proceed.

I have tried to run step 2 as (although, I am not if that is the correct way of doing this)

MCPB.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__MCPB.py&d=DwQGaQ&c=Oo8bPJf7k7r_cPTz1JF7vEiFxvFRfQtp-j14fFwh71U&r=NgCylDEQBE0axDv2CZqG8l4J7GJcRRTGkieutsHMLXQ&m=EMp4riidrcIh5KcbPrtmPEZo_bDyz9JjWBjXqG5WcPLLMDn9rKfh__-La70kpOJa&s=RwUaHkOgk5QCDQ2-41T6HUT4qZY2zGTr5jH-MB-s8-c&e=> -i caco3.in<https://urldefense.proofpoint.com/v2/url?u=http-3A__caco3.in&d=DwQGaQ&c=Oo8bPJf7k7r_cPTz1JF7vEiFxvFRfQtp-j14fFwh71U&r=NgCylDEQBE0axDv2CZqG8l4J7GJcRRTGkieutsHMLXQ&m=EMp4riidrcIh5KcbPrtmPEZo_bDyz9JjWBjXqG5WcPLLMDn9rKfh__-La70kpOJa&s=HuGLW8IrOKGoZzLcvGK6Fs6n9Nnd_dEYmmATwa74MiM&e=> -s 2 --logf caco3_small_fc.log

With this command, and even without the --logf option, I receive the following message:

FileNotFoundError: [Errno 2] No such file or directory: 'caco3_small_opt.fchk'

As far as I understood, the .fchk file is a gaussian file. What am I missing here?

I appreciate any help.

Sincerely,
Felipe Silva Carvalho
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Received on Wed Oct 23 2024 - 13:30:02 PDT
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