[gmx-users] Residue name length

[András Ferenc WACHA]

Dear Justin,

thank you for your reply. Five characters is the limit then.

Andras

On 2/4/19 3:48 PM, Justin Lemkul wrote:
>
>
> 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.
>
> -Justin
>
>> 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,
>>
>> Andras
>>
>
-- 
András Ferenc Wacha, PhD
research fellow, CREDO instrument responsible

Biological Nanochemistry Research Group

Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences
Hungarian Academy of Sciences (RCNS HAS)
Magyar tudósok körútja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.mta.hu, 
CREDO SAXS instrument: http://credo.ttk.mta.hu


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