[gmx-users] Re: Nanotubes with Tubegen

[Christopher Stiles]

>>Christopher Stiles wrote:
>> 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.
> 
>you can try either -r or -o but you don't need the rtp anyway. note that 
>you can use the pbc flag to get an infinite CNT.
> 
>-- 
>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 <http://www.gromacs.org/mailman/listinfo/gmx-users>
spoel at gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users>
http://folding.bmc.uu.se

 

 

 

I am not 100% sure how I should respond to these (as in format) but let me
know if there is a preferred method.

 

Ok what I am trying to do is use the *.top and the *.rtp file with pdb2gmx
to make my *.gro file to use with editconf and genbox ect. I take it there
is a better/easier way to do this?

 

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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