[gmx-users] carbon nano tubes pdb file

[Justin A. Lemkul]

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

-- 
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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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