hello every one i have been removed all the error of previous output but still i got one new error Fatal error: [ file strong_posre.itp, line 3886 ]: Atom index (3882) in position_restraints out of bounds (1-3881). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule.
i have been changed the position_restrints but no out put same error please help topol.top ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include "strong_posre.itp" #endif ; Include ligand topology #include "drag.itp" ; Include POPC chain topology #include "popc.itp" ; Include water topology #include "gromos53a6_lipid.ff/spc.itp" On Thu, Jul 10, 2014 at 10:46 AM, RINU KHATTRI <nickname.mi...@gmail.com> wrote: > hello every one > ohk i havbben pasted UNK portion from old files because it is still > missing in system.gro now after running minimization i got new error old > problem has resolved > :-) grompp (-: > > Option Filename Type Description > ------------------------------------------------------------ > -f minim.mdp Input grompp input file with MD parameters > -po mdout.mdp Output grompp input file with MD parameters > -c system_inflated.gro Input Structure file: gro g96 pdb tpr etc. > -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. > -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. > -n index.ndx Input, Opt. Index file > -p topol.top Input Topology file > -pp processed.top Output, Opt. Topology file > -o confout.tpr Output Run input file: tpr tpb tpa > -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt > -e ener.edr Input, Opt. Energy file > > Option Type Value Description > ------------------------------------------------------ > -[no]h bool no Print help info and quit > -[no]version bool no Print version info and quit > -nice int 0 Set the nicelevel > -[no]v bool no Be loud and noisy > -time real -1 Take frame at or first after this time. > -[no]rmvsbds bool yes Remove constant bonded interactions with > virtual > sites > -maxwarn int 2 Number of allowed warnings during input > processing. Not for normal use and may generate > unstable systems > -[no]zero bool no Set parameters for bonded interactions without > defaults to zero instead of generating an error > -[no]renum bool yes Renumber atomtypes and minimize number of > atomtypes > > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8# > Generated 813 of the 2346 non-bonded parameter combinations > > ERROR 1 [file topol.top, line 22752]: > No default Proper Dih. types > > Excluding 3 bonded neighbours molecule type 'Protein_chain_A' > Excluding 3 bonded neighbours molecule type 'UNK' > Excluding 3 bonded neighbours molecule type 'POPC' > > NOTE 1 [file topol.top, line 24831]: > System has non-zero total charge: 14.788998 > Total charge should normally be an integer. See > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > for discussion on how close it should be to an integer. > > > There was 1 note > > ------------------------------------------------------- > Program grompp, VERSION 4.5.5 > Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line: > 1388 > > Fatal error: > There was 1 error in input file(s) > > kindly help > > > > On Thu, Jul 10, 2014 at 10:17 AM, RINU KHATTRI <nickname.mi...@gmail.com> > wrote: > >> hello gromacs users >> ohk justin but if unk is deleted then how to put it back in >> system_inflate.gro >> >> >> On Wed, Jul 9, 2014 at 5:16 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >>> >>> >>> On 7/9/14, 6:17 AM, RINU KHATTRI wrote: >>> >>>> hello every one >>>> I am working on complex with popc membrane i did >>>> >>>> perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat >>>> >>>> after this step minimization >>>> >>>> grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr >>>> >>>> i got error >>>> Fatal error: >>>> number of coordinates in coordinate file (system_inflated.gro, 10224) >>>> does not match topology (topol.top, 10245) >>>> i have been removed 6 lipid molecules in my topology file according to >>>> output i got one thing new in my system_inflate.gro file the written >>>> displayed atom is 10224 but after counting it is 10536 so if i correct >>>> it >>>> difference is more >>>> >>> >>> I don't know what this means, but the number of atoms that grompp is >>> finding is going to be correct. >>> >>> >>> in topology file [molecule] >>>> protein chain 1 >>>> UNK 1 >>>> POPC 122 >>>> how to resolve it >>>> >>> >>> I would venture a guess that UNK has 21 atoms. I don't know that >>> InflateGRO handles arbitrary molecules, so it may have gotten deleted upon >>> inflation. Check system_inflated.gro; it will be very obvious if it is >>> missing. >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> ================================================== >>> -- >>> 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.
