[gmx-users] Atomtype:CB

[Haberl Florian]

Hi,
>
> 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???

Normally i use gromacs forcefield (gmx) and put correct files from prodrg
server

DRGFIN.GRO  : final coordinates in GROMOS87 format
DRGGMX.ITP  : GROMACS .itp file

and in pdb2gmx gmx as forcefield.

Greetings,

Florian


>
> highly appreciate your input.
>
> nancy
>
>
> ----- 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
>
>
> Hi
>>
>> 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
>
>
> Greetings,
>
> Florian
>
> ------------------------------------------------------------------------
>  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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------------------------------------------------------------------------
 Florian Haberl              Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen

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

------------------------------------------------------------------------