Re: [gmx-users] gromacs: pdb2gmx error
On 26/02/2012 3:13 PM, venkatesh s wrote: Thanking you Mark Abraham for your valuable suggestion Here i used DNA Ligand Complex only is that any specific options is there? Please consider the advice here http://www.gromacs.org/Support about the kind of content that requests for help should have in order to maximize the chance that someone might be able to help you. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] gromacs: pdb2gmx error
Thanking you Mark Abraham for your valuable suggestion Here i used DNA Ligand Complex only is that any specific options is there? Thanks -- *S.VENKATESH,* II M.Sc Bioinformatics, Alagappa University, Karaikudi-630003 Tamil Nadu, India svenkateshbioinformat...@gmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs: pdb2gmx error
On 25/02/2012 6:30 PM, venkatesh s wrote: Hi i got that error in the step of pdb2gmx what can i do i read also http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database can any one tell exact reason and how i handle further The exact reason is on that link. You will need to read it and think about what it means. If it doesn't mean anything, then you need to learn some more in chapter 5 of the manual (and/or the links in that web page section) about how things work. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] gromacs: pdb2gmx error
Hi i got that error in the step of pdb2gmx what can i do i read also http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database can any one tell exact reason and how i handle further thanking you - All occupancies are one Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp Atomtype 1 Reading residue database... (oplsaa) Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp Residue 56 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.4# Processing chain 1 'E' (603 atoms, 20 residues) Identified residue DG2 as a starting terminus. Warning: Residue MN1022 in chain has different type (Other) from starting residue DG2 (DNA). Identified residue DT20 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.5.5 Source code file: resall.c, line: 581 Fatal error: Residue 'DG' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- *S.VENKATESH,* II M.Sc Bioinformatics, Alagappa University, Karaikudi-630003 Tamil Nadu, India Mobile Phone:- 9486494616 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
