[gmx-users] n2t file format for similar atoms

Justin Lemkul jalemkul at vt.edu
Wed May 6 23:17:14 CEST 2015

On 5/6/15 1:22 PM, jwillcox at andrew.cmu.edu wrote:
> Hello,
> I'm trying to specify two different hydroxyl hydrogen atoms in the n2t
> format:
> H    opls_988    0.435   1.0079 1    O 0.0945
> and
> H    opls_117    0.4238  1.008   1   O 0.1
> for a hydroxyl group on graphene and water, respectively.
> When performing x2top, it seems to assume all Hs in the system are defined
> by whichever set of parameters is listed first.  I tried using alternate
> atom labels, e.g. HG and HW, but it gave the same problem.  Is there a way
> to separate the two different hydrogen types?

The simplest approach is to not use x2top for writing a water topology.  It 
should be straightforward to write the water topology and #include it in the 
.top (or simply use one of the existing models).

Likely what's happening is that x2top is matching the first instance of any H 
that matches the distance criterion (within 10% of the specified distance).  I 
bet if you reverse the appearance of the H lines in the .n2t, you'd get the 
opposite parameters assigned.  You could modify the x2top code to be more 
permissive if you like, but the simplest solution is what I said above - don't 
ask x2top to do something complex when the molecule isn't complex :)



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


More information about the gromacs.org_gmx-users mailing list