Thanks for reply ,The problem is solved .The problem was with topology file .
On Fri, Jun 4, 2010 at 4:44 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > jani vinod wrote: > >> Hello, >> I build a system solvated in water . >> Then replicated the system using genconf. Now when I am running grompp i >> am >> getting following warning >> Warning: atom name 404 in PH7.top and replicate_systemB.gro does not match >> (N - C1) >> Warning: atom name 405 in PH7.top and replicate_systemB.gro does not match >> (H1 - C2) >> Warning: atom name 406 in PH7.top and replicate_systemB.gro does not match >> (H2 - C3) >> Warning: atom name 407 in PH7.top and replicate_systemB.gro does not match >> (H3 - N4) >> Warning: atom name 408 in PH7.top and replicate_systemB.gro does not match >> (CA - C5) >> Warning: atom name 409 in PH7.top and replicate_systemB.gro does not match >> (CB - C6) >> Warning: atom name 410 in PH7.top and replicate_systemB.gro does not match >> (CG - O7) >> Warning: atom name 411 in PH7.top and replicate_systemB.gro does not match >> (OD1 - P8) >> Warning: atom name 412 in PH7.top and replicate_systemB.gro does not match >> (OD2 - O9) >> Warning: atom name 413 in PH7.top and replicate_systemB.gro does not match >> (C - O10) >> Warning: atom name 414 in PH7.top and replicate_systemB.gro does not match >> (O - O11) >> Warning: atom name 415 in PH7.top and replicate_systemB.gro does not match >> (N - C12) >> Warning: atom name 416 in PH7.top and replicate_systemB.gro does not match >> (H - C13) >> Warning: atom name 417 in PH7.top and replicate_systemB.gro does not match >> (CA - O14) >> Warning: atom name 418 in PH7.top and replicate_systemB.gro does not match >> (CB - C15) >> Warning: atom name 419 in PH7.top and replicate_systemB.gro does not match >> (C - O16) >> Warning: atom name 420 in PH7.top and replicate_systemB.gro does not match >> (O - C17) >> Warning: atom name 421 in PH7.top and replicate_systemB.gro does not match >> (N - C18) >> Warning: atom name 422 in PH7.top and replicate_systemB.gro does not match >> (H - C19) >> Warning: atom name 423 in PH7.top and replicate_systemB.gro does not match >> (CA - C20) >> >> and when after ignoring the warning I try to run system my system get >> distorted. >> >> > Whenever grompp throws warnings like this, don't ignore them and plow > ahead, it's a recipe for disaster. The [molecules] section of your topology > is out of order with respect to your coordinate file, so parameters for > different species are being applied incorrectly. > > -Justin > > >> Thanks >> vinod >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 >
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