Vigneshwar Ramakrishnan wrote:
Hi All,
I am a newbie to GROMACS, so pardon me if I am wrong.
I think pdb2gmx can handle this with amber forcefields. We just need to
use the right nomenclature. I think the .hdb files for amber ff in
GROMACS are already equipped with the necessary info.
I am not sure why one must use an external software for adding the
hydrogen atoms.
If I am wrong, pls correct me.
No you're both (potentially) right.
On Fri, May 2, 2008 at 12:09 AM, Justin A. Lemkul <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
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.
If the port of the AMBER force fields to GROMACS have suitable .hdb
files, then pdb2gmx can deal with the problem.
Mark
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