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

[Justin Lemkul]

On 5/3/16 5:21 PM, Nash, Anthony wrote:
> 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?
>

No.  Names are read from the reference coordinates and nothing else (since 
trajectories don't have atom name information, anyway).

-Justin

> 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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-- 
==================================================

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

==================================================