[gmx-users] Error in Topology file

[Justin Lemkul]

On 1/21/15 7:59 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 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
> https://www.dropbox.com/sh/rtxg36y4pv2zwto/AADoQ_Y239XuSXK7-_4PNGJ_a?dl=0
>
> 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?
>

You have two lines that conflict:

H    opls_168    0.000  1.0080  1    O 0.096
H    opls_117    0.410  1.0080  1    O 0.100

g_x2top can't distinguish between the two (since both reference distances 
overlap, within the ± 10% criterion), so it picks the first that it finds. 
Hence your waters get messed up.

-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

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