[gmx-users] g_hbond

[Justin Lemkul]

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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