[gmx-users] Atomtype:CB

Nancy Deng jdeng at adrik.bchs.uh.edu
Mon Mar 14 19:15:12 CET 2005

Hi Haberl,

thank you so much for the quick response. I use "GROMOS96 43a1 Forcefield
(official disctibution)" to generate protein .gro and .top. The ligand files
(drg.itp, and DRGFIN.gro) were from the server. From the "readme" file, i
noticed that a comment for DRGFIN.gro: final coordinates in GROMOS87 format.
Is this what you said the ff problem???

Would you mind more suggestions how to fix???

highly appreciate your input.


----- Original Message ----- 
From: "Haberl Florian" <Florian.Haberl at chemie.uni-erlangen.de>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Monday, March 14, 2005 9:56 AM
Subject: Re: [gmx-users] Atomtype:CB

> 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.

Have you taken always the same forcefield, seems you mixed them up.
Readme from prodrg output gives you correct information about ff - file



 Florian Haberl              Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen

 Mailto: florian.haberl AT chemie.uni-erlangen.de

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