[gmx-users] PROBLEM REGARDING pdb2gmx & restraints

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jun 28 12:31:41 CEST 2007

Hi Gurpreet,

1. http://wiki.gromacs.org/index.php/GROMOS (note term "united atom")
2. http://wiki.gromacs.org/index.php/Manual:grompp_3.3.2 (check -r)

In addition, read Chapter 5 of the manual, regarding topologies (and
the file format, #include statements and "position_restraints")

Wow.., that wiki makes replying easy :)



On 6/28/07, gurpreet singh <gps.iitm at gmail.com> wrote:
> hello gromacs users
>  my question is regarding the command pdb2gmx which is the first step to
> process ur input file. i used the force field 43a1 and i m doing some
> dimeric protein simulation . when i checked the output of the pdb2gmx
> command i found that this command have not added any hydrogens to the carbon
> atoms of the protein although to  other heavy atoms hydrogens were added.
>  is it the usual behaviour of gromacs or there is some other mistake in
> giving the command ?
>  pdb2gmx -ff G43a1 -ignh -posrefc 50 -f input.pdb -p toplo.top -o output.pdb
> -i posre.itp -water spce
>  my second question is about the positional restraints. since i have the
> dimer so after using the pdb2gmx i got the two posre_A.itp & posre_B.itp
> files for putting the restriants,
>  i am little bi doubltful about the way we use these files for maintaing the
> restraints
>  i used in the following way
>  grompp -f input.mdp  -c somefile.pdb -p toplo.top -r
> posre_A.itp,posre_B.itp -o output.tpr
>  is this the right way to mention the restaints or not ?
>  and if i want to change the restraints gradually after each step of the
> simulation then what is the procedure to do that ?
>  Gurpreet singh
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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