[gmx-users] Adding Hydrogens by pdb2gmx
jmsstarlight at gmail.com
Mon Oct 31 13:23:50 CET 2011
Its very unclear for me because after pdb2gmx -f 1.pdb -o conf.gro -ignh
with gromos force field
I've checked conf.gro by VMD and this structure didnt contains any
2011/10/31 Justin A. Lemkul <jalemkul at vt.edu>
> James Starlight wrote:
>> Dear Gromacs Users!
>> I could not find how I can add missing hydrogens after their removing by
>> pdb2gmx -ignh.
>> I have modified structure of my protein after editing by some soft and I
>> removed all hydrogens but now I want to add it back in accordance with
>> gromos ff topology
>> How I can do it ?
> They are removed and rebuilt entirely by pdb2gmx in accordance with the
> instructions found in the .hdb file. If there are no hydrogens in the
> input, then -ignh is irrelevant.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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