[gmx-users] problem with pdb2gmx

Stud_Psychopharm stu_psyc at nimhans.kar.nic.in
Fri Nov 21 05:57:01 CET 2003

Dear Sergio,
when doing pdb2gmx, it will ask you to select the forcefield, select "0" 
there. while running editconf give the following command:
editconf -f *.pdb or gro -d 0.8 -c -o out.gro
genbox -cp out.gro -cs -p *.top -o *.pdb

and do the other steps.
It workedout for me after the similar problem.
All the best
blaise m costa.
"The more we learn the more we realize how little we know." - 
R.Buckminster Fuller 

Blaise M.
Graduate Student,
Department of Psychopharmacology,
National Institute of Mental Health And Neuro Sciences (NIMHANS),
India. Tel: 91 80 6995112.

-----Original Message-----
From: "Sergio E. Wong" <swon9 at itsa.ucsf.edu>
To: gmx-users at gromacs.org
Date: Thu, 20 Nov 2003 20:24:49 -0800 (PST)
Subject: [gmx-users] problem with pdb2gmx

> Dear Sirs;
>   I'm new to gromacs.  I'm trying to set up a system for simulation. 
> The
> pdb code is 2RCS.  I use pdb2gmx initially to get a topology file, I
> use
> the -his option interactively decide the positions of the histidine
> hydrogens (all have both hydrogens).  After that I used genbox to
> produce
> a water box and I used the option -box 10 10 10.  Then I used genion to
> add 8 anions.  Then I realize that I need to use pdb2gmx to produce a
> new
> topology file that includes the anions.  So, I try to use it, but on
> CYS214, the input .gro file reads CYSH (it has the thiol hydrogen),
> however, I get an error message complaining about the thiol hydrogen
> and
> it says that it can't find that hydrogen in the .rtf file for CYS2. 
> For
> some reason, it doesn't read the file properly and thinks that the
> residue
> type is CYS2 rather than CYSH.  I'm using the OPLS force field.  Any
> suggestions would be appreciated.
> Thanks
> -Sergio
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