[gmx-users] Re: carbon nano tubes pdb file

[Vitaly Chaban]

> 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


Please, use x2top for tubes.

-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA