VMD-L Mailing List

From: Denilson F. Oliveira (denilson_at_dqi.ufla.br)
Date: Fri Dec 02 2016 - 12:03:00 CST

Dear João,

I will provide answers right after your questions to make understanding
easier:

1) Was the chlorine atom defined as "Cl" in the str file?

Yes. "Cl" was used in the str and pdb files.

2) Is this str file made by you or is it an original file from the
CHARMM force field?

I made it.

3) I would be careful to change the name of the to "CL" as this atom is
declared in the lipid topology.

Yes. I know it. But I could not find another solution for this problem.
Therefore, I make sure that my str file is the last parameter file to be
read by Namd, so that in my calculation "CL" will be treated as a
chlorine atom. It is not a very strange solution as chlorine is named
"CL" in CGenFF 3.0.1. By the way, to use "CL" to name different atoms in
the lipid topology and CGenFF will certainly generate some problems.

Best wishes.

Denilson

Em 02-12-2016 13:10, João Ribeiro escreveu:
> Dear Denilson,
>
> Was the chlorine atom defined as "Cl" in the str file? Is this str
> file made by you or is it an original file from the CHARMM force field?
>
> I would be careful to change the name of the to "CL" as this atom is
> declared in the lipid topology file as
>
> "MASS 145 CL 12.011000 C ! carbonyl C (acetic acid/methyl acetate)"
>
> The definition for the chlorine atom in the CHARMM that I could find
> is in the file "toppar_all36_prot_aldehydes.str"
> "MASS -1 CLAL 35.45300 ! Chlorine Atom"
>
> Also, if you are looking for the chloride ion, it is defined in the
> "toppar_water_ions.str" file, with the atom name CLA.
> "MASS -1 CLA 35.45000 CL ! Chloride Ion"
>
> Best wishes
>
> Joao
>
> On Fri, Dec 2, 2016 at 5:53 AM Denilson F. Oliveira
> <denilson_at_dqi.ufla.br <mailto:denilson_at_dqi.ufla.br>> wrote:
>
> Dear all,
>
> I have found a small problem in both VMD 1.9.2 and 1.9.3:
>
> 1) Chlorine atoms in my pdb and str files were named "Cl".
>
> 2) These files were used as input for the Autopsf plugin, which
> generated the corresponding pdb and psf files without any problem.
> In the generated files chlorine atoms were also named "Cl".
>
> 3) The pdb and psf generated files were used as input for the
> Solvate plugin that converted the coordinates of all chlorine
> atoms to zero (x=0 , y=0, z=0).
>
> To avoid this problem chlorine atoms must be named "CL" in the
> original pdb and str files.
>
> Best wish.
>
> Denilson.
>
>
> --
> Dr. Denilson F. Oliveira
> Professor Titular
> Laboratório de Produtos Naturais
> Departamento de Química
> Universidade Federal de Lavras
> Caixa Postal 3037
> Lavras-MG-Brasil
> CEP 37.200-000
> Tel: (55) (35) 3829-1623
> Fax: (55) (35) 3829-1812
> e-mail:denilson_at_dqi.ufla.br <mailto:denilson_at_dqi.ufla.br>
>