> 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
