[gmx-users] Atomtype:CB

[Nancy Deng]

Dear All,

I applied the PRODRG server to get the ligand files (drg.itp, DRGFIN.gro)
for gramacs input. In drg.itp file, there are several carbon atoms were
recognized correctly as atomtype CB. (I'm running gromacs on linux cluster.)

After edit the recepter-protein.gro and .top as suggested by the tutorial, I
started to run "grompp" to generate a .trp file. However, the grompp was
killed with fatal error of " Atomtype CB could not found".

I know from the tutorial, the "CB" is "legal" atom type among the 47 list.

So, I  am just wondering whether you have any experience or suggestions to
help me out.

Thanks you very much,

nancy
----- Original Message ----- 
From: <mprabha at fiu.edu>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Monday, March 14, 2005 8:29 AM
Subject: Re: [gmx-users] Nanotube simulation


> I genarate cnt from tubegen program It is a public domain program. I used
prodrg or x2mtop to create the topoly file. Anyhow you have to tune various
parameters. Don't use to pdb2gmx but use x2mtop to genarate topology
> >
> > From: Ignacio Rodriguez Fernandez <irf at soton.ac.uk>
> > Date: 2005/03/14 Mon AM 10:15:14 EST
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] Nanotube simulation
> >
> > Hi all,
> >
> > Is there anywhere I can find the residue types for a carbon nanotube?
> >
> > Has anybody built a PDB file for a carbon nanotube that GROMACS can
read?
> >
> > In NAMD the residue type is "ARM" ( obtained at
> > http://www.ks.uiuc.edu/Training/Tutorials/#nanotubes ) , but GROMACS
does
> > not recognize it!
> >
> > It neither understands the type "UNK" (unknown) created by the program
> > "tubegen":
http://deaddog.duch.udel.edu/~frey/research/tubegenonline.html
> >
> > Thanks.
> >
> > --
> > Ignacio Rodriguez Fernandez
> >
> > Computational Engineering & Design Research Group
> > School of Engineering Sciences
> > University of Southampton
> > Southampton SO17 1BJ
> > United Kingdom
> >
> > Location: Building 25, room 1035
> > Phone: +44 (0) 23 8059 3637
> > email: irf at soton.ac.uk
> >
> >
> >
> >
> >
> >
> >
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