[gmx-users] Energy minimization

Yang Ye leafyoung81-group at yahoo.com
Wed Jan 11 15:57:36 CET 2006

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

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