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
