[gmx-users] minor edits to a .gro file

[Justin Lemkul]

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

-- 
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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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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