hello everyone my grompp related problem atomtype CA not found has been solved now i am using 56a3 force field for protein ligand complex with popc but srill i didnt get em.tpr a new error
Excluding 3 bonded neighbours molecule type 'POPC' Excluding 2 bonded neighbours molecule type 'SOL' ------------------------------------------------------- Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (popc128.gro, 14036) does not match topology (topolpopc.top, 17459) kindly help On Wed, Jul 2, 2014 at 3:51 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/2/14, 6:07 AM, RINU KHATTRI wrote: > >> hello gromacs users >> i used 43a1 force field(Gromacs 4.5.7) in the atomtype.atp file in the >> place of CA CA2+ is present in ffnonbonded.itp file CA and CA2+ both are >> present according to tutorial i have been followed all the step >> still em.tpr not formed >> atomtype CA not found >> >> > "CA" is the gmx.ff nomenclature for the calcium type, so that suggests > you're mixing and matching force fields (note that gmx.ff has been removed > from the latest Gromacs version, since it should not be used). Without > explicit detail of your topology (i.e. post your files so they can be > downloaded), there's very little that can be done to suggest where things > have gone wrong. I strongly suspect you've mixed and matched force fields > somewhere, which is easy to do when dealing with complex systems. Pick a > force field, stick to it exactly. > > -Justin > > > >> On Wed, Jul 2, 2014 at 3:19 PM, ERASTOVA V. < >> valentina.erast...@durham.ac.uk >> >>> wrote: >>> >> >> Hi Rinu, >>> >>> See what forcefield files you include in your topology, then go to the >>> force field folders and check if those indeed have that atom types. >>> You must indeed be missing the CA type. Likely, you just forgot to >>> include >>> some topology file. >>> >>> V >>> >>> >>> >>> >>> On 2 Jul 2014, at 10:23, gromacs.org_gmx-users-request@ >>> maillist.sys.kth.se >>> <mailto:gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: >>> >>> >>> ------------------------------ >>> >>> Message: 2 >>> Date: Wed, 2 Jul 2014 12:26:07 +0530 >>> From: RINU KHATTRI <nickname.mi...@gmail.com<mailto: >>> nickname.mi...@gmail.com>> >>> To: gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org> >>> Subject: [gmx-users] error in grompp command >>> Message-ID: >>> <caoefx3kbphak_brp4l4orcp_gsbsusohnlughx0wyjwewua...@mail.gmail.com >>> <mailto:CAOEfx3KBphAK_BRP4L4orCp_gSBsuSOHNLUgHX0WyJweWuaN9A@ >>> mail.gmail.com >>> >>>> >>>>> Content-Type: text/plain; charset=UTF-8 >>> >>> hello gromacs >>> i an working on protein ligand complex with lipid membrane (popc) >>> >>> grompp -f minim.mdp -c popc128.gro -p topol_popc.top -o em.tpr -maxwarn >>> -1 >>> >>> after this fatal error atomtypes CA not found >>> and only md.oonly mdout is formed >>> kindly help >>> >>> >>> ------------------------------ >>> >>> -- >>> 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. >>> >>> > -- > ================================================== > > 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.