[gmx-users] Error in grompp steps of position restrained

[Mark Abraham]

On 8/06/2012 12:34 PM, Malai wrote:
> Dear Mark,
>
> Thanks for mail. you mean I need to define in mdp file?.

No. Using one of the two ways I suggested earlier depend what you're 
actually trying to do, but since your intention in using the CA group is 
unknown to us, you're preventing yourself getting specific help.

> Can you please guide me how to do that. Thanks.

http://www.gromacs.org/Documentation/File_Formats/Index_File

Mark
>
> On Fri, Jun 8, 2012 at 10:30 AM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 8/06/2012 12:23 PM, Malai wrote:
>
>         Hi,
>
>         After Successfully neutralizing and sd minimization of the
>         system, I got the below error when I try the grompp for
>         position restrained step. The command I used is :grompp -v -f
>         eqn1.mdp -c complx_sd.pdb -p complx.top -o complx_eqn1.tpr
>
>         Any help will be highly appreciated.
>
>         Many thanks.
>
>
>         Error message:
>
>         -------------------------------------------------------
>         Program grompp, VERSION 4.5.5
>         Source code file: readir.c, line: 1320
>
>         Fatal error:
>         Group CA not found in index file.
>         Group names must match either [moleculetype] names
>         or custom index group names,in which case you
>         must supply an index file to the '-n' option of grompp.
>         For more information and tips for troubleshooting, please
>         check the GROMACS
>         website at http://www.gromacs.org/Documentation/Errors
>         -------------------------------------------------------
>
>
>     Your .mdp file referred to a group for which grompp could find no
>     definition. Choose a better group or make a definition.
>
>     Mark
>     -- 
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