[gmx-users] PDB files

[soumadwip ghosh]

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.

Soumadwip
Research Fellow,
IITB
India