Re: [gmx-users] error group protein not found
Hi, if there is a protein in your system you should have protein as standard group. Maybe you use a template mdp file in which the temperature coupling group is protein. if you have no protein in your simulation check the mdp files for tc-grps and adjust accordingly. Max On Jun 3, 2015, at 3:07 PM, Victor Rosas Garcia rosas.vic...@gmail.com wrote: Hello, In your command line you do not specify an index file. Maybe you need to generate one. Check out usage of make_ndx. Hope this helps Victor 2015-06-03 13:41 GMT-05:00 marzieh dehghan dehghanmarz...@gmail.com: Hi every body I create a covalent bond and now I want to held MD by gromacs, after holding the following command : grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr I confornted to an error: Fatal error: Group Protein 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. please let me know how can I solve this problem. I am looking forward to getting your answer thanks a lot -- *Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and Biophysics (IBB)University of Tehran, Tehran- Iran.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error group protein not found
Hello, In your command line you do not specify an index file. Maybe you need to generate one. Check out usage of make_ndx. Hope this helps Victor 2015-06-03 13:41 GMT-05:00 marzieh dehghan dehghanmarz...@gmail.com: Hi every body I create a covalent bond and now I want to held MD by gromacs, after holding the following command : grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr I confornted to an error: Fatal error: Group Protein 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. please let me know how can I solve this problem. I am looking forward to getting your answer thanks a lot -- *Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and Biophysics (IBB)University of Tehran, Tehran- Iran.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] error group protein not found
Hi every body I create a covalent bond and now I want to held MD by gromacs, after holding the following command : grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr I confornted to an error: Fatal error: Group Protein 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. please let me know how can I solve this problem. I am looking forward to getting your answer thanks a lot -- *Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and Biophysics (IBB)University of Tehran, Tehran- Iran.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
