sreelakshmi ramesh wrote:
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 <http://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..
The best place to start for all problems is to search the mailing list archive.
This error comes up almost every week, and at least several times a year
regarding CNT. I'll save you a few minutes and have you look here:
http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database
For specifics about CNT and how to deal with them, refer to:
http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube
Some of the information is out of date, but there are posts in the archive that
walk through almost all of the necessary information (again I say: search the
archive). Don't use pdb2gmx; it doesn't handle non-linear molecules well.
g_x2top is a much better option.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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