[gmx-users] generating gro files using pdb2gmx without adding hydrogen

Kai Zhuang kai.zhuang at gmail.com
Thu May 19 18:13:03 CEST 2005

for pdb2gmx, you can specify the protonation state of LYS, ASP, GLU,
CYS, HIS or the terminal COO-/NH3+
check manual for the detail, i read about it a while ago, haven't used
it yet.   u can turn on ineractive selection for these by -inter
but other than this, i believe gromacs adds the Hs according to its
itp file definition.  if it doesn't work, try find out how to change
the itp file
Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com

On 19 May 2005 07:06:39 -0000, balamurugan r <biobee at rediffmail.com> wrote:
>    Dear Sir,
>              I have to run MD simulation for a protein under certain pH and
> i have added the hydrogens to the pdb file accordingly using BUILDER module
> in InsightII.  
>            Now i have the pdb file with required hydrogens added and i want
> to generate a gro file but i dont want pdb2gmx to add further hydrogens to
> my pdb file.
>            What are my options?
>  Balamurugan
>  Bioinformatics Centre
>  Pondicherry University
>  India
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