Re: no Na or CLA paramters in par_all22_prot.inp

From: Peter Freddolino (
Date: Mon Mar 27 2006 - 09:39:30 CST

Dear Shulin,
you can probably just use the par_all27_prot_na.prm parameters for your
simulations, since those par27 files actually contain charmm22
parameters for protein and charmm27 parameters for lipid/nucleic acid
(as you'll find in the header of the file), and are considered
compatible. In your case, it is safe to either copy those parameters
over to par_all22, or just to use of of the par27 files, as the protein
parameters are the same in either case.

Shulin Zhuang wrote:

> Dear All,
> I use top_all22_prot.inp for the setup of psf file and use
> par_all22_prot.inp to make the configuration file for the
> minimization. My protein is neutralized with three chloride ions(CLA)
> using VMD, however, there are no parameters for CLA in
> par_all22_prot.inp. How should I do?
> Should I simply copy the CLA parameter from par_all27_prot_lipid.inp
> or par_all27_prot_na.prm. But this does not seem appropriate>
> Waiting any suggestions.
> best regards
> --
> Shulin Zhuang
> Chemistry Department
> Zhejiang University PRC
> <>

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