[gmx-users] Nanotubes with Tubegen

[Christopher Stiles]

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

 

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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