Re: [gmx-users] problem in energy minimisation during inflategro process.
Hi, In addition to Mark's comments: > ; Include chain topologies > #include "rr1_A.itp" > #include "rr1_B.itp" > > ; Include position restrain protein > #ifdef POSRES_PROTEIN > #include "rr1_A_pr.itp" > #include "rr1_B_pr.itp" > #endif > This is rubbish. Position restraints are defined as part of molecule types. You can't include them outside the scope of a [ molecule_type ] block. You'll get the 'invalid order of directives' error for that. You have to include the position restraint include files in the respective molecule definition include files. Understanding how topologies and coordinates are put together is vital when doing anything already slightly out of the ordinary. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] problem in energy minimisation during inflategro process.
nitu sharma wrote: Dear Justin but even after doing this when i I have tried to do second step of inflategro i.e energy minimisation step I got the error like this-- Fatal error: number of coordinates in coordinate file (inflated_dmpc.pdb, 13253) does not match topology (inflated_dmpc.top, 15395) --- So can you suggest me what possible modification make it successfully completed. please If you have any idea let me know. This is a pretty explicit error message. The existence of the list doesn't absolve you of the need to think about what you are doing and what might have gone wrong :-) Here, you need to observe what is in the coordinate file, compare that with what is in the .top file, and see what is causing a 2000-atom discrepancy. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] problem in energy minimisation during inflategro process.
Dear Justin I am doing inflategro process for scaling and packing of lipid around my protein . the first step is successfully completed ,there is 9 lipid removed a/c to that I have updated my topology file --- ; Include forcefield parameters #include "ffG53a6_lipid.itp" ; Include chain topologies #include "rr1_A.itp" #include "rr1_B.itp" ; Include position restrain protein #ifdef POSRES_PROTEIN #include "rr1_A_pr.itp" #include "rr1_B_pr.itp" #endif ; Include generic topology for ions #include "ions.itp" ; Include DMPC chain topology #include "dmpc.itp" [ system ] ; Name Protein in DMPC bilayer [ molecules ] ; Namenumber Protein_A 1 Protein_B 1 DMPC 119 NA+1 I have removed also water molecule infomation becoz in inflated system there is no water molecule but even after doing this when i I have tried to do second step of inflategro i.e energy minimisation step I got the error like this-- Fatal error: number of coordinates in coordinate file (inflated_dmpc.pdb, 13253) does not match topology (inflated_dmpc.top, 15395) --- So can you suggest me what possible modification make it successfully completed. please If you have any idea let me know. Thanks a lot justin for solving my problem. Nitu Sharma School of life Sciences Jawaherlal Nehru university New delhi, India --More--(94%) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
