[gmx-users] Error in Topology file

Rajan Kumar kumarrajan513 at gmail.com
Wed Jan 21 14:00:14 CET 2015

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 one side of the Graphene sheet. Also I have added water
molecules in form of spherical droplet on the same side of the sheet.

I used the following commands to generate .gro and  topology file.

editconf -f GO.pdb -o conf.gro -box 3 3 3 -angles 90 90 90

g_x2top -f conf.gro -o topol.top -ff oplsaa_GO

My topology file is generated, but it show that there is a overall
charge in the system, which I didn't expect.
All files can be accessed at

So,I opened my topology file and I see

328   opls_116      2    SOL     OW    328      -0.82     15.999   ; qtot -0.82
329   opls_168      2    SOL    HW1    328          0      1.008   ; qtot -0.82
330   opls_168      2    SOL    HW2    328          0      1.008   ; qtot -0.82

I have two different type of hydrogen in my .atp file, one for 'OH' on
Graphene and other for water molecule. I have also specified their
separate connectivity and chrages in .n2t file.
However, from my topology file, I see that only one type of hydrogen
atom (i.e. one corresponding to 'OH' of graphene, which doesn't have
any charge) is present in topology file, due to which there is overall
charge on the system.

Any idea why this might be happening?

Rajan Kumar
Indian Institute of Technology, Guwahati

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