[gmx-users] pdb2gmx

[mirko busato]

Thank you very much,

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 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 ?

Thank you very much

Mirko


On Wednesday, June 25, 2014 12:00 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
 




On 6/25/14, 4:44 AM, mirko busato wrote:
> Thank you very much,
>
> In my analysis ,I would like to consider Hydrogen bonds involving S atom as well.  I think that g_hbond is not built to manage Hydrogen bonds with S.
>
> Do you know if there are available scripts? or Could you suggest me something to solve this problem?
>

g_hbond is hard-coded to deal with certain groups, so it's not very flexible. 
The workaround we've used in the past is to simply rename the S atoms of 
interest as O in the .top file, generate a .tpr with those dummy names, and run 
g_hbond using that .tpr file.


-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

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