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

Malai winterhot82 at gmail.com
Fri Jun 8 04:34:45 CEST 2012

Dear Mark,

Thanks for mail. you mean I need to define in mdp file?. Can you please
guide me how to do that. Thanks.

On Fri, Jun 8, 2012 at 10:30 AM, Mark Abraham <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
>> website at http://www.gromacs.org/**Documentation/Errors<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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