[gmx-users] PDB files

[Justin Lemkul]

On 5/29/15 5:38 AM, soumadwip ghosh wrote:
> Hi all,
>        I have a general query about PDB files. I have made a PDB file for a
> carbon nanotube (15x15) using VMD which contains 1600 carbon atoms. As far
> as I know, the PDB file should contain atom no. in lines 13-16 and the
> residue id in line 18-20. Now,I obtained the pdb file from VMD as follows-
> ATOM    993 C    UNK     1       6.595   7.749  40.611  1.00  0.00
> ATOM    994 C    UNK     1       8.477   5.630  40.611  1.00  0.00
> ATOM    995 C    UNK     1       9.179   4.394  40.611  1.00  0.00
> ATOM    996 C    UNK     1      10.034   1.692  40.611  1.00  0.00
> ATOM    997 C    UNK     1      10.172   0.278  40.611  1.00  0.00
> ATOM    998 C    UNK     1       9.855  -2.538  40.611  1.00  0.00
> ATOM    999 C    UNK     1       9.405  -3.886  40.611  1.00  0.00
> ATOM   1000 C    UNK     1       7.968  -6.329  40.611  1.00  0.00
> ATOM   1001 C    UNK     1       7.009  -7.378  40.611  1.00  0.00
> ATOM   1002 C    UNK     1       4.702  -9.025  40.611  1.00  0.00
> ATOM   1003 C    UNK     1       3.399  -9.592  40.611  1.00  0.00
> ATOM   1004 C    UNK     1       0.622 -10.157  40.611  1.00  0.00
> ATOM   1005 C    UNK     1      -0.799 -10.145  40.611  1.00  0.00
> ATOM   1006 C    UNK     1      -3.566  -9.531  40.611  1.00  0.00
> ATOM   1007 C    UNK     1      -4.859  -8.941  40.611  1.00  0.00
> ATOM   1008 C    UNK     1      -7.136  -7.255  40.611  1.00  0.00
> ATOM   1009 C    UNK     1      -8.077  -6.190  40.611  1.00  0.00
> ATOM   1010 C    UNK     1      -9.471  -3.722  40.611  1.00  0.00
> ATOM   1011 C    UNK     1      -9.897  -2.366  40.611  1.00  0.00
> ATOM   1012 C    UNK     1     -10.166   0.455  40.611  1.00  0.00
> ATOM   1013 C    UNK     1     -10.004   1.867  40.611  1.00  0.00
> ATOM   1014 C    UNK     1      -9.101   4.553  40.611  1.00  0.00
> ATOM   1015 C    UNK     1      -8.378   5.777  40.611  1.00  0.00
> ATOM   1016 C    UNK     1      -6.460   7.863  40.611  1.00  0.00
>   and so on. Now my question is, if I make a topology, whether by pdb2gmx or
> by topology builders such as SWISSPARAM, do I need to number carbon atoms
> like C1, C2 ,C3 in the third column of the pdb? It is difficult since
> numbering carbon atoms would lead to the third column from line # 13-17
> once the index goes pass 999. Why I asking this is I am trying to build the
> topology of this nanotube using SWISSPARAM. I am converting this pdb to
> mol2 format and upload it on the server but the job in SWISSPARAM fails and
> it complains about the numbering of carbon atoms should have been like C1,
> C2, C3 and so on. I am using CHARMM force field and thats why I cant use
> g_x2top either for building the topology of a carbon  nanotube or graphene
> at all in any conventional method. Any help in this regard will be most
> appreciated.
>

I don't see how using CHARMM prevents you from using x2top.  That's the 
appropriate tool for the job.  You'll need to write an .n2t file, but with a 
graphene sheet, CNT, etc. that are all C atoms at regular spacing, it takes one 
line.  See http://www.gromacs.org/Documentation/File_Formats/.n2t_File

-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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