[gmx-users] Graphene topology file

[Justin Lemkul]

On Mon, Aug 4, 2014 at 8:38 AM, #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg>
wrote:

> Hi gromacs users,
>
> I was able to simulate graphene sheet in water. Now I want to simulate
> functionalised graphene sheet with -OH groups attached randomly to graphene
> sheet. I modified atomname2type.n2t file by adding oxygen and hydrogen
> groups to it. Following is my .n2t file:
>
> C    opls_995    0      12.011  2    C  0.142  C 0.142
> C    opls_996    0      12.011  3    C  0.142  C 0.142  C 0.142
> C    opls_997    0      12.011  1    C  0.142
> C    opls_998    0      12.011  4    C  0.142  C 0.142  C 0.142  O 0.143
> OH  opls_154  -0.7    15.9994 2    C  0.143  HO 0.96
> HO  opls_155   0.435  1.008   1    OH  0.96
>
> But when I give following x2top command, I get error message :
>
> g_x2top -f grap1.pdb -o graphene.top -name  GRA -nexcl 3 -pbc
>
> Error:
> Fatal error:
> Could only find a forcefield type for 256 out of 456 atoms
>
> Can anyone please let me know what can be creating the problem?
>
>
g_x2top will print to the screen all of the atoms that it had problems
with.  The error means that either your distance criteria are wrong or the
geometry of the system is otherwise incompatible with the specifications in
the .n2t file.

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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