Re: [gmx-users] error in grompp command
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.commailto: nickname.mi...@gmail.com To: gmx-us...@gromacs.orgmailto: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.
Re: [gmx-users] error in grompp command
, 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.commailto: nickname.mi...@gmail.com To: gmx-us...@gromacs.orgmailto: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.
Re: [gmx-users] error in grompp command
...@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.commailto: nickname.mi...@gmail.com To: gmx-us...@gromacs.orgmailto: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. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- 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.
Re: [gmx-users] error in grompp command
On 7/3/14, 6:27 AM, RINU KHATTRI wrote: 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 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 In this case, the warnings about non-matching names are harmless and they refer only to different conventions in water nomenclature. You can easily re-name the atoms in the coordinate file with simple sed statements, but it's not necessary here. Ignoring mismatching names in other cases can be very harmful, so be advised. em.tpr is formed but rest of the files are not formed What other files are you looking for? The purpose of grompp is to produce a .tpr file; there are other files that can be produced, but none of them are essential. -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.
[gmx-users] error in grompp command
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.
[gmx-users] error in grompp command
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-requ...@maillist.sys.kth.semailto: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.commailto:nickname.mi...@gmail.com To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org Subject: [gmx-users] error in grompp command Message-ID: caoefx3kbphak_brp4l4orcp_gsbsusohnlughx0wyjwewua...@mail.gmail.commailto:caoefx3kbphak_brp4l4orcp_gsbsusohnlughx0wyjwewua...@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.
Re: [gmx-users] error in grompp command
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-requ...@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.commailto: nickname.mi...@gmail.com To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org Subject: [gmx-users] error in grompp command Message-ID: caoefx3kbphak_brp4l4orcp_gsbsusohnlughx0wyjwewua...@mail.gmail.com mailto:caoefx3kbphak_brp4l4orcp_gsbsusohnlughx0wyjwewua...@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.
