Begin forwarded message:
From: [EMAIL PROTECTED]
Date: June 17, 2006 2:53:27 AM EDT
To: "Pradip Kumar Biswas" <[EMAIL PROTECTED]>
Subject: Re: QMMM calculation
Dear Sir,
Thank you for your kind reply. Which force field should I use for my
calculation. I have seen you using OPLS for your calculation. Is it
possible to use Gromos force field, where polar hydrogen is used.
You should be able to use any force field implemented or supported by Gromacs. QM/MM does not depend upon the force field.
If all
atom force field in not taken, then no of atoms will reduce in CPMD for QM
calculation.
I could not really get what you mean. The number of QM atoms in CPMD will be coming from the [QM] section of the index.ndx file of Gromacs. First you need to create an index.ndx file in the usual Gromacs way and then manually add the [QM] section where you mention your desired atom ids. The rest of the atoms of your system will go to CPMD as an external field where you can manipulate their number by setting up a qmmmcoulomb_cutoff (pl. see the other posting today).
I am facing problem in generating the gro & itp files for my ligands in
OPLS force field.
Please figure out the way for generating parameters file for my
non-standard residue using OPLS FF.
If you are comfortable with Gromos FF, go ahead with that.
Thanking you,
with regards,
amit
--
Pradip K. Biswas, PhD.
Research Associate, Department of Chemistry;
Cleveland State University, Ohio-44115
Phone: 1-216-875-9723
http://comppsi.csuohio.edu/groups/people/biswas.html
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