[gmx-users] Error in topology using g_x2top

[Rajan Kumar]

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.

-- 
Rajan Kumar
Indian Institute of Technology, Guwahati