[gmx-users] Energy minimization

[Yang Ye]

perhaps you shall read more than just the instruction but focus on 
what's the problematic atom in your .pdb file.

Yang Ye

Dhananjay wrote:

> Hello all,
>
> I want to perform energy minimization and not MD.
> A  .pdb  file is with me and using programme "protonate"  the 
> hydrogens has been added to it.
> Now I want to perform energy minimization on this file.
> When I tried pdb2gmx to form topology file , the programme asked to 
> ignore hydrogens using  -ignh .
>
> Will it ignore all the added hydrogens ?
>
> If I want to generate .top file incluging added hydrogens, is it 
> possible in any way ?
>
> -- Dhananjay
>
>------------------------------------------------------------------------
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>

-- 
/Regards,/
Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Singapore
Tel: 6316-2884
/