hello gromacs users now have been removed this error after changing the number of SOL in topol_popc.top file (counted from popc128.gro) after that i hav used -maxwarn 1 command
result is Generated 813 of the 2346 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'POPC' Excluding 2 bonded neighbours molecule type 'SOL' Warning: atom name 6657 in topolpopc.top and popc128.gro does not match (OW - OW1) Warning: atom name 6658 in topolpopc.top and popc128.gro does not match (HW1 - HW2) Warning: atom name 6659 in topolpopc.top and popc128.gro does not match (HW2 - HW3) Warning: atom name 6660 in topolpopc.top and popc128.gro does not match (OW - OW1) Warning: atom name 6661 in topolpopc.top and popc128.gro does not match (HW1 - HW2) Warning: atom name 6662 in topolpopc.top and popc128.gro does not match (HW2 - HW3) Warning: atom name 6663 in topolpopc.top and popc128.gro does not match (OW - OW1) Warning: atom name 6664 in topolpopc.top and popc128.gro does not match (HW1 - HW2) Warning: atom name 6665 in topolpopc.top and popc128.gro does not match (HW2 - HW3) Warning: atom name 6666 in topolpopc.top and popc128.gro does not match (OW - OW1) Warning: atom name 6667 in topolpopc.top and popc128.gro does not match (HW1 - HW2) Warning: atom name 6668 in topolpopc.top and popc128.gro does not match (HW2 - HW3) Warning: atom name 6669 in topolpopc.top and popc128.gro does not match (OW - OW1) Warning: atom name 6670 in topolpopc.top and popc128.gro does not match (HW1 - HW2) Warning: atom name 6671 in topolpopc.top and popc128.gro does not match (HW2 - HW3) Warning: atom name 6672 in topolpopc.top and popc128.gro does not match (OW - OW1) Warning: atom name 6673 in topolpopc.top and popc128.gro does not match (HW1 - HW2) Warning: atom name 6674 in topolpopc.top and popc128.gro does not match (HW2 - HW3) Warning: atom name 6675 in topolpopc.top and popc128.gro does not match (OW - OW1) Warning: atom name 6676 in topolpopc.top and popc128.gro does not match (HW1 - HW2) (more than 20 non-matching atom names) WARNING 1 [file topolpopc.top, line 26]: 7380 non-matching atom names atom names from topolpopc.top will be used atom names from popc128.gro will be ignored Analysing residue names: There are: 128 Other residues There are: 2460 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 34725.00 Largest charge group radii for Van der Waals: 0.216, 0.216 nm Largest charge group radii for Coulomb: 0.216, 0.216 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 54x54x60, spacing 0.116 0.114 0.115 Estimate for the relative computational load of the PME mesh part: 0.36 This run will generate roughly 164 Mb of data There was 1 warning how tom resolve these problems em.tpr is formed but rest of the files are not formed help On Thu, Jul 3, 2014 at 2:23 PM, RINU KHATTRI <nickname.mi...@gmail.com> wrote: > 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.
