[gmx-users] carbon nano tubes pdb file

[sreelakshmi ramesh]

Dear all,
              I need to create a starting pdb file for doble walled Carbon
nano tube of desired radius with two graphene sheets.I already have one but
when i use pdb2gmx  gromacs The pdb file looks something like this..

RYST1    0.000    0.000    0.000  90.00  90.00  90.00 P 1           1
ATOM      1  C1  C04 X   1     -14.016 -14.520  -5.439  0.00  0.00
Q1
ATOM      2  C2  C04 X   1     -15.177 -15.176  -5.439  0.00  0.00
Q1
ATOM      3  C3  C04 X   1     -15.172 -16.503  -5.439  0.00  0.00
Q1
ATOM      4  C4  C04 X   1     -14.064 -17.290  -5.439  0.00  0.00
Q1
ATOM      5  C1  C04 X   1     -11.705 -14.546  -5.439  0.00  0.00
Q2
ATOM      6  C2  C04 X   1     -12.862 -15.229  -5.439  0.00  0.00
Q2
ATOM      7  C3  C04 X   1     -12.884 -16.614  -5.439  0.00  0.00
Q2
ATOM      8  C4  C04 X   1     -11.728 -17.307  -5.439  0.00  0.00
Q2
ATOM      9  C1  C04 X   1      -9.390 -14.555  -5.439  0.00  0.00      Q3
*pdb2gmx -f carbon.pdb -o out.pdb -p topol.top *
its just a part of pdb i had attached the complete pdb file.i am able to
view this in vmd.it fine.but when i do pdb2gmx it gives me the following
error with charmm force field or any other force fields..

Processing chain 1 'X' (4765 atoms, 225 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Warning: Starting residue C041 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue C66B1 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue C66B2 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue C66B3 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue C66B4 in chain not identified as Protein/RNA/DNA.
More than 5 unidentified residues at start of chain - disabling further
warnings.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully

-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.3
Source code file: resall.c, line: 581

Fatal error:
Residue 'C04' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



any help please..

regards,
sree.
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