Dear all,<br> 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..<br>
<br>RYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1<br>ATOM 1 C1 C04 X 1 -14.016 -14.520 -5.439 0.00 0.00 Q1 <br>ATOM 2 C2 C04 X 1 -15.177 -15.176 -5.439 0.00 0.00 Q1 <br>
ATOM 3 C3 C04 X 1 -15.172 -16.503 -5.439 0.00 0.00 Q1 <br>ATOM 4 C4 C04 X 1 -14.064 -17.290 -5.439 0.00 0.00 Q1 <br>ATOM 5 C1 C04 X 1 -11.705 -14.546 -5.439 0.00 0.00 Q2 <br>
ATOM 6 C2 C04 X 1 -12.862 -15.229 -5.439 0.00 0.00 Q2 <br>ATOM 7 C3 C04 X 1 -12.884 -16.614 -5.439 0.00 0.00 Q2 <br>ATOM 8 C4 C04 X 1 -11.728 -17.307 -5.439 0.00 0.00 Q2 <br>
ATOM 9 C1 C04 X 1 -9.390 -14.555 -5.439 0.00 0.00 Q3 <br><b>pdb2gmx -f carbon.pdb -o out.pdb -p topol.top </b><br>its just a part of pdb i had attached the complete pdb file.i am able to view this in <a href="http://vmd.it">vmd.it</a> fine.but when i do pdb2gmx it gives me the following error with charmm force field or any other force fields..<br>
<br>Processing chain 1 'X' (4765 atoms, 225 residues)<br>There are 0 donors and 0 acceptors<br>There are 0 hydrogen bonds<br>Warning: Starting residue C041 in chain not identified as Protein/RNA/DNA.<br>Warning: Starting residue C66B1 in chain not identified as Protein/RNA/DNA.<br>
Warning: Starting residue C66B2 in chain not identified as Protein/RNA/DNA.<br>Warning: Starting residue C66B3 in chain not identified as Protein/RNA/DNA.<br>Warning: Starting residue C66B4 in chain not identified as Protein/RNA/DNA.<br>
More than 5 unidentified residues at start of chain - disabling further warnings.<br>Problem with chain definition, or missing terminal residues.<br>This chain does not appear to contain a recognized chain molecule.<br>If this is incorrect, you can edit residuetypes.dat to modify the behavior.<br>
8 out of 8 lines of specbond.dat converted successfully<br><br>-------------------------------------------------------<br>Program pdb2gmx, VERSION 4.5.3<br>Source code file: resall.c, line: 581<br><br>Fatal error:<br>Residue 'C04' not found in residue topology database<br>
For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br><br><br><br>any help please..<br>
<br>regards,<br>sree.<br><br><br>