[gmx-users] Re: Nanotubes with Tubegen

[David van der Spoel]

Christopher Stiles wrote:
>>>Christopher Stiles wrote:
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>>>/ RE: gmx-users Digest, Vol 39, Issue 25, 4/
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>>>/ /
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>>>/ It wasn't apparent to me that it was so simple, I copied the ffgmx.n2t file/
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>>>/ from the GMXLIB to my working dir and renamed it to ffG43b1.n2t and it/
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>>>/ worked just fine with x2top. One catch though/
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>>>/ /
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>>>/ When I use x2top with the following command:/
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>>>/ /
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>>>/ x2top -f testH.pdb -o testH.top -r testH.rtp/
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>>>/ /
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>>>/ it does not create the testH.rtp file, but does properly make the testH.top/
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>>>/ file./
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>>>/ /
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>>>/ So my question is there a trick or does it go some where else or maybe it/
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>>>/ just will not do it for my SWCNT/
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>>>/ /
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>>>/ Also I have searched the archives and found this problem popped up many/
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>>>/ other times bit no solution is given that I can locate./
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>> 
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>>you can try either -r or -o but you don't need the rtp anyway. note that 
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>>you can use the pbc flag to get an infinite CNT.
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>> 
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>>-- 
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>>David van der Spoel, Ph.D.
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>>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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>>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
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> I am not 100% sure how I should respond to these (as in format) but let 
> me know if there is a preferred method.
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> 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?
> 
You can use pdb and gro files for any tool in gromacs. If you have top 
file you don't need to run pdb2gmx.

-- 
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