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

[Malai]

Dear MARK,

> 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.
>

The error is CA index file. So my intention is to use CA group and avoid
the error. please suggest me how to use grompp or make CA index file for
grompp in position restrained step.


>
>
>  Can you please guide me how to do that. Thanks.
>
>
> http://www.gromacs.org/Documentation/File_Formats/Index_File
>

so i need to make index files for CA atoms of protein using make_ndx for
CA. can you please explain how to make index file for CA using make_ndx.

Thanks for help.


>
> Mark
>
>
> 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
>>> 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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>
>
>
>
>
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