[gmx-users] Re: Nanotubes with Tubegen

[Christopher Stiles]

RE: gmx-users Digest, Vol 39, Issue 25, 4

It wasn't apparent to me that it was so simple, I copied the ffgmx.n2t file
from the GMXLIB to my working dir and renamed it to ffG43b1.n2t and it
worked just fine with x2top. One catch though

When I use x2top with the following command:

x2top -f testH.pdb -o testH.top -r testH.rtp

it does not create the testH.rtp file, but does properly make the testH.top
file.

So my question is there a trick or does it go some where else or maybe it
just will not do it for my SWCNT

Also I have searched the archives and found this problem popped up many
other times bit no solution is given that I can locate.

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


>>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