[gmx-users] Energy minimization

Dhananjay dhananjay.c.joshi at gmail.com
Wed Jan 11 07:47:04 CET 2006

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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