[gmx-users] graphene top file

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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