[gmx-users] Residue name length
jalemkul at vt.edu
Mon Feb 4 15:48:44 CET 2019
On 2/2/19 8:15 AM, András Ferenc WACHA wrote:
> Dear Gromacs users (or developers),
> does anyone know if there is a limitation on the maximum length of
> residue names? The reason I'm asking this is that I am trying to build
> residue topologies for disubstituted beta-amino acids with proteinogenic
> sidechains. My current nomenclature covers all such beta-amino acids in
> at most 7 characters (including the most obscure ones). First of all: is
> there an input coordinate format which supports this? .gro and .g96
> support at most 5 characters, .pdb only 3. Secondly, if there would be
The maximum in any format in GROMACS is 5 characters.
> such a format, can the MD code choke on long residue names due to some
> hard-wired limit in the code?
mdrun doesn't care at all about residue or atom names. It cares about
physical properties, and it only uses name information when writing the
final coordinate file at the end of the run.
> If the limit is five, what other possibilities do I have? Are residue
> names case sensitive, for instance (e.g. B2a and B2A are considered the
> same or not)?
> Thank you for your help,
Justin A. Lemkul, Ph.D.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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