On 6/9/16 2:40 PM, Nash, Anthony wrote:
Hi all,
I¹m looking to open a .gro file, add in six hydrogen dummy atoms (I can
rename the atom name/type, I just need the correct x, y and z coords) to
the end of an amino acid sidechain and save whilst preserving as much of
the .gro format as it can.
I would normally load the crystal/derived structure as a .pdb into
Avogadro or smaller fragments from Gaussian output. Unfortunately, as I
have defined a completely bespoke post-translation amino acid I can¹t
restore to .pdb with the aim of using Avogadro, too much can go wrong.
Recommendations for Gromacs friendly editing tools would be appreciated.
Easy way: fire up your favorite text editor and do it yourself.
Harder way: write an .rtp and .hdb entry for your custom residue and process
with pdb2gmx and it will build the H positions according to the .hdb entry.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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