[gmx-users] Energy minimization

MGiò magiofer at gmail.com
Wed Jan 11 10:35:08 CET 2006

you'd better protonate your protein with pdb2gmx, using the -ignh and -arg,
-his, -glu ... tags to choose the protonation of each polar residue, then
you should have no problems creating your topology file.

I wish it helps,

On 1/11/06, Dhananjay <dhananjay.c.joshi at gmail.com> 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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