[gmx-users] Error in topology using g_x2top

[Justin Lemkul]

On 12/24/14 1:39 AM, Rajan Kumar wrote:
> Hi all,
>
> I am trying to study wetting of water on Graphene oxide(GO). My
> structure has functional group in form of Hydroxyl and epoxide group
> on only one side of the Graphene sheet. Also I have added water
> molecules in form of spherical droplet on the same side of the sheet.
> Since my simulation will be periodic in the plane of the GO sheet, I
> have not capped edges with hydrogen.
>
> I have created atomtypes.atp and atomname2type.n2t based on
> connectivity of individuals atoms and added them to force field
> file(oplsaa_GO.ff) in the working directory(Thanks Justin Lemkul for
> Suggestion). Also, I have copied original opls-aa ffnonded and
> ffnonbonded topology files to my working directory.
> Have a look at my files here
> https://www.dropbox.com/sh/rtxg36y4pv2zwto/AADoQ_Y239XuSXK7-_4PNGJ_a?dl=0
>
> After creating .gro using editconf, I generate topology using g_x2top
> which gives me following error.
>
> g_x2top -f conf.gro -o topol.top -ff oplsaa_GO
>
> Opening force field file ./oplsaa_GO.ff/atomname2type.n2t
> There are 11 name to type translations in file ./oplsaa_GO.ff
> Generating bonds from distances...
>
>   atom 420
> Can not find forcefield for atom OS-9 with 5 bonds
> Can not find forcefield for atom OH-10 with 8 bonds
> Can not find forcefield for atom HO-11 with 8 bonds
> Can not find forcefield for atom OS-20 with 11 bonds
> Can not find forcefield for atom OH-21 with 16 bonds
> Can not find forcefield for atom HO-22 with 10 bonds
> Can not find forcefield for atom OS-31 with 12 bonds
> Can not find forcefield for atom OH-32 with 10 bonds
> Can not find forcefield for atom HO-33 with 13 bonds
> Can not find forcefield for atom OS-42 with 6 bonds
> Can not find forcefield for atom OH-43 with 13 bonds
> ----------------------------------------------------
> ----------------------------------------------------
> Can not find forcefield for atom OS-325 with 4 bonds
> Can not find forcefield for atom OH-326 with 7 bonds
> Can not find forcefield for atom HO-327 with 8 bonds
> -----------------------------------------------------
> ------------------------------------------------------
> Can not find forcefield for atom HW2-414 with 13 bonds
> Can not find forcefield for atom OW-415 with 4 bonds
> Can not find forcefield for atom HW1-416 with 3 bonds
> Can not find forcefield for atom HW2-417 with 2 bonds
> Can not find forcefield for atom OW-418 with 20 bonds
> Can not find forcefield for atom HW1-419 with 9 bonds
> Can not find forcefield for atom HW2-420 with 6 bonds
>
> -------------------------------------------------------
> Program g_x2top, VERSION 4.5.5
> Source code file: g_x2top.c, line: 206
>
> Fatal error:
> Could only find a forcefield type for 238 out of 420 atoms
>
> Please help me out here.
>

Something is very bizarre with the input coordinates or the .n2t file, but a 
quick look at the files doesn't suggest what it is.  If g_x2top is detecting 20 
(yikes!) bonds for a water oxygen atom, that suggests something is 
catastrophically wrong somewhere.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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