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 <[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<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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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