[gmx-users] Nanotubes with Tubegen

[David van der Spoel]

Christopher Stiles wrote:
>  
> 
> I am trying to do a simulation involving a SWCNT generated by Tubegen 
> (http://turin.nss.udel.edu/research/tubegenonline.html) . Then I use 
> Chimera to add hydrogen to the end carbon atoms (I did this because it 
> was given as a possible solution in of the articles I ran across, 
> although I have tried it both with hydrogen and without resulting in the 
> same outcome). And I got testH.pdb from this…
> 
>  
> 
> I tryed to run pdb2gmx using the following command:
> 
>  
> 
> pdb2gmx -f testH.pdb -p testH.top -o testH.gro
> 
>  
> 
> I get the following error when selecting 1: GROMOS96 43b1 vacuum force 
> field:
> 
>  
> 
> Program pdb2gmx, VERSION 3.3.1
> 
> Source code file: resall.c, line: 438
> 
>  
> 
> Fatal error:
> 
> Residue 'UNK' not found in residue topology database
> 
>  
> 
> Then if I try to use x2top instead using the following command:
> 
>  
> 
> I get the following error when selecting 1: GROMOS96 43b1 vacuum force 
> field:
> 
>  
> 
> Program x2top, VERSION 3.3.1
> 
> Source code file: futil.c, line: 537
> 
>  
> 
> Fatal error:
> 
> Library file ffG43b1.n2t not found in current dir nor in default 
> directories.
> 
> (You can set the directories to search with the GMXLIB path variable)
> 
>  
> 
>  
> 
> In my library there only exists one file with a n2t extension and it is 
> ffgmx.n2t
> 
>  
and did you try this one?

> 
> So well I have spent countless hours reading and looking through the 
> entirety web resources to no avail. So I am hoping for a hand to point 
> me in the correct direction.
> 
>  
> 
> Thank you very much for your help!
> 
> ~Christopher Stiles
> 
> College of Nanoscale Science and Engineering (CNSE)
> 
> State University of New York, Albany, New York 12203, USA
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se