On 10/27/14 2:21 PM, fatemeh ramezani wrote:
Dear gmx-users
I built a graphene sheet (graphene.pdb ) by VMD. I convert it to gro file with
editconf command. Then I made top file with g_x2top command. But in top file
connection between atoms is not correct(highlighted lines below). How can I
solve this problem?
I see no highlighting.
Connection in pdb file for 12 atoms;
CONECT 1 2
CONECT 2 1 3
CONECT 3 2 4
CONECT 4 3
CONECT 5 6
CONECT 6 5 7
CONECT 7 6 8
CONECT 8 7
CONECT 9 10
CONECT 10 9 11
CONECT 11 10 12
Connection in top file for these atoms;
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
1 6 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
1 1936 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
2 3 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
2 81 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
3 4 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
3 84 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
4 7 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
4 85 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05
5 6 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
5 10 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05
5 1940 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
6 7 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
7 8 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
8 11 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05
8 89 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05
9 10 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
9 14 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
9 1944 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
10 11 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
11 12 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05
CONECT records are irrelevant for basically all Gromacs tools. The bonds
created by g_x2top are decided upon based on the criteria specified in the force
field's .n2t file. Based on the snippet you've shown, I see nothing wrong.
-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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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