[gmx-users] g_saltbr analysis

[Justin Lemkul]

On 7/12/14, 3:29 AM, elham tazikeh wrote:
> Dear users
> i used of *g_saltbr* for Amyloid Beta Peptide with Zinc cation simulation
> and aquired 3 outputs :min-min.xvg, plus-min.xvg , plus-plus.xvg
>
> there are 5 salt bridges between His 6 , Glu 11 - His13 , Glu 11- His 14 ,
> Glu 11- His 13 , His 14 and also between Asp 23 , Lys 28
>
> in this issue, i can not use of above outputs and i dont know how analyze
> those files?

g_saltbr produces a rather large dump of files that are hard to parse.  If you 
know of specific interactions you want to monitor over time, just measure 
distances with g_dist.

-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

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