[gmx-users] gmx hbond - specify precise atom names involved

[Nash, Anthony]

Thanks Justin,


I’ll give that a try. I assume this approach would still require the .trr
to be converted to a .gro file, and then the customised names
‘search-replaced’ with the respective ‘fake’ names?

Thanks
Anthony

On 03/05/2016 16:22, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Justin Lemkul"
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
jalemkul at vt.edu> wrote:

>
>
>On 5/3/16 9:16 AM, Nash, Anthony wrote:
>>
>> Hi all,
>>
>> Can gmx hbond accept user specified atoms for the donors (default OH and
>> NH) and acceptor (default O and N)? I don¹t seem to find any mention of
>> this in the -help text.
>>
>
>It's hard-coded in the source, so it's rather inflexible.
>
>> I have a post-trans modified protein from a rather bulk cross-linked
>> peptide chain. I defined unique atom times but I have used a unique set
>>of
>> atom names.
>>
>
>Create a "fake" topology that uses O,N,H as the first character in
>applicable 
>atom names.  Then run the analysis using this .tpr file.  We did this a
>while 
>back with, e.g. thiols and a few others.
>
>-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
>
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
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