[gmx-users] adding missing hydrogen in PDB files

[Justin A. Lemkul]

In terms of external software, check out OpenBabel:
http://openbabel.org/wiki/Main_Page

There's also the H++ server, which employs Babel as part of its algorithm:
http://biophysics.cs.vt.edu/H++/index.php

I believe H++ can handle nucleic acids.  You could also do all of this with
Gromacs, if you can come up with relevant entries in the .hdb file for your
particular force field.  Then pdb2gmx could produce the right structure with
added hydrogens.

-Justin

Quoting Arijit Maitra <arijitmaitra at yahoo.com>:

> Hi All
>
> I have been trying to simulate a DNA tetramer
> d(GGGGTTTTGGGG)_2 using gromacs with amber ports. I
> have downloaded the X-ray structure from
> www.rcsb.org/pdb which has several missing hydrogen
> atoms. Can anybody advise how to plug in the missing
> atoms, e.g. with softwares or otherwise to proceed
> with the pdb2gmx command?
>
> Thanks
> Ari
>
>
>
>
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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