[gmx-users] CNT

[Justin A. Lemkul]

Quoting Hero <cjt0610 at yahoo.com>:

> Hello,
>
> I plan  to insert water molecules into a Single Wall NanoTube,
> I have generated the structure file of SWNT, but when I use:
>
>    pdb2gmx -f SWNT_6_6_144.pdb -p SWNT.top -o SWNT.gro
>
> to form the gro file, I got the following error:
>
>    Fatal error:
>    Residue 'UNK' not found in residue topology database

pdb2gmx is not magic; see here:

http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database

There is also a very detailed link about CNT preparation that was provided to
you earlier across this list:

http://cs86.com/CNSE/SWNT.htm

-Justin

>
> Could you please help me out?
>
> Thank you very much!
>
> Jue
>
>
>
>
>
>
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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