[gmx-users] g_hbond

[Erik Marklund]

Hi,

I think this may actually be a bug. g_hbond reports zero contacts in cases where I know there are many. Will examine this more thoroughly and file a redmine issue.

Kind regards,
Erik


Erik Marklund, PhD
Postdoctoral Research Associate

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

On 14 Jul 2014, at 13:24, mirko busato <busato.mirko at yahoo.com> wrote:

> thank you very much,
> I read the manual of g_mindist but seem produce in output only the number of contacts and the minimum distance .
> 
> For my problem I would like to know all the atoms involved  (all the contacts) within of 4 Å.
> 
> so I can understand which atoms can do salt bridge interactions.
> 
> Do you know a way to do this with g_mindist command?
> Thank you very much,
> Mirko
> 
> 
> On Monday, July 14, 2014 2:02 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> 
> 
> On 7/14/14, 7:44 AM, mirko busato wrote:
>> Dear Users,
>> 
>> I have one question for you. I would  like to  extract some information about salt bridge interactions (without using the gromacs command  g_saltbr  because it gave me some problems) between some atoms (charged negatively) of a type of monomer and some atoms (charged positively )of another type of monomer.
>> 
>> So I created the two lists of atoms with g_select,
>> and I made a file index like that:
>> 
>> [ N_CRL ]
>>    300  321  342  363  384  405  426  447  468  489  510  531  552  573  594
>>    615  636  657  678  699  720  741  762  783  804  825  846  867  888  909
>>    930  951  972  993 1014 1035 1056 1077 1098 1119
>> [ OX_ITA ]
>>    168  181  194  207  220  233  246  259  272  285
>> 
>> and then I used g_hbond to extract the contacts of these 2 lists of atoms within 4 Å.
>> 
>> in this way:
>> 
>> g_hbond_d -f eq4.gro -s eq3.tpr -n index.ndx -hbn hbond.ndx -contact -r2 0.4 -r 0.4
>> 
> 
> I wouldn't use g_hbond like this; g_mindist -on is more straightforward for 
> calculating simple contacts.
> 
> 
>> 
>> I noticed a strange thing, if I change the order of the groups in the index.ndx file,like that:
>> 
>> [ OX_ITA ]
>>    168  181  194  207  220  233  246  259  272  285
>> [ N_CRL ]
>>    300  321  342  363  384  405  426  447  468  489  510  531  552  573  594
>>    615  636  657  678  699  720  741  762  783  804  825  846  867  888  909
>>    930  951  972  993 1014 1035 1056 1077 1098 1119
>> 
>> I obtain no contacts, and it is wrong because actually I didn't change the atoms of the groups.
>> 
>> Could you help me about it ?
> 
> Order of the groups in the index file is irrelevant; it doesn't seem likely that 
> this is the only issue.
> 
> -Justin
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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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