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 <[email protected]
<mailto:[email protected]>> 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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