Sorry to disturb you again. It would be of immense help if you could please help me with this one. During energy minimization with gmx mdrun -v -deffnm em ; I did not get any results. The earlier code run was gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr and I used em.mdp file provided there. Is there something wrong the em.mdp file I used? ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.2 ; long range electrostatic cut-off vdwtype = cutoff vdw-modifier = force-switch rvdw-switch = 1.0 rvdw = 1.2 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions DispCorr = no
On Fri, Oct 11, 2019 at 6:58 PM Suprim Tha <shrestha.suprim...@gmail.com> wrote: > I had .pdb as extra. I finally got it right. Thanks a ton sir. > > On Fri, Oct 11, 2019 at 6:55 PM Suprim Tha <shrestha.suprim...@gmail.com> > wrote: > >> The error is still the same. I changed the name to JZ4. Please see what I >> am missing again. >> * Toppar stream file generated by >> * CHARMM General Force Field (CGenFF) program version 2.2.0 >> * For use with CGenFF version 4.0 >> * >> read rtf card append >> * Topologies generated by >> * CHARMM General Force Field (CGenFF) program version 2.2.0 >> * >> 36 1 >> ! "penalty" is the highest penalty score of the associated parameters. >> ! Penalties lower than 10 indicate the analogy is fair; penalties between >> 10 >> ! and 50 mean some basic validation is recommended; penalties higher than >> ! 50 indicate poor analogy and mandate extensive validation/optimization. >> RESI JZ4.pdb 0.000 ! param penalty= 0.900 ; charge penalty= >> 0.342 >> GROUP ! CHARGE CH_PENALTY >> ATOM C4 CG331 -0.271 ! 0.285 >> ATOM C7 CG2R61 -0.108 ! 0.000 >> ATOM C8 CG2R61 -0.113 ! 0.000 >> ATOM C9 CG2R61 -0.109 ! 0.000 >> ATOM C10 CG2R61 0.105 ! 0.190 >> ATOM C11 CG2R61 -0.115 ! 0.000 >> ATOM C12 CG2R61 -0.009 ! 0.232 >> ATOM C13 CG321 -0.177 ! 0.342 >> ATOM C14 CG321 -0.184 ! 0.045 >> ATOM OAB OG311 -0.529 ! 0.190 >> ATOM H7 HGR61 0.115 ! 0.000 >> ATOM H8 HGR61 0.115 ! 0.000 >> ATOM H9 HGR61 0.115 ! 0.000 >> ATOM H11 HGR61 0.115 ! 0.000 >> ATOM H132 HGA2 0.090 ! 0.000 >> ATOM H133 HGA2 0.090 ! 0.000 >> ATOM H142 HGA2 0.090 ! 0.000 >> ATOM H143 HGA2 0.090 ! 0.000 >> ATOM HAB HGP1 0.420 ! 0.000 >> ATOM H41 HGA3 0.090 ! 0.000 >> ATOM H42 HGA3 0.090 ! 0.000 >> ATOM H43 HGA3 0.090 ! 0.000 >> BOND C4 C14 >> BOND C4 H41 >> BOND C4 H42 >> BOND C4 H43 >> BOND C7 C8 >> BOND C7 C11 >> BOND C7 H7 >> BOND C8 C9 >> BOND C8 H8 >> BOND C9 C10 >> BOND C9 H9 >> BOND C10 C12 >> BOND C10 OAB >> BOND C11 C12 >> BOND C11 H11 >> BOND C12 C13 >> BOND C13 C14 >> BOND C13 H132 >> BOND C13 H133 >> BOND C14 H142 >> BOND C14 H143 >> BOND OAB HAB >> END >> read param card flex append >> * Parameters generated by analogy by >> * CHARMM General Force Field (CGenFF) program version 2.2.0 >> * >> ! Penalties lower than 10 indicate the analogy is fair; penalties between >> 10 >> ! and 50 mean some basic validation is recommended; penalties higher than >> ! 50 indicate poor analogy and mandate extensive validation/optimization. >> BONDS >> ANGLES >> DIHEDRALS >> CG321 CG2R61 CG2R61 OG311 2.4000 2 180.00 ! JZ4.pdb , from CG311 >> CG2R61 CG2R61 OG311, penalty= 0.6 >> CG2R61 CG321 CG321 CG331 0.0400 3 0.00 ! JZ4.pdb , from >> CG2R61 CG321 CG321 CG321, penalty= 0.9 >> IMPROPERS >> END >> RETURN >> >> @<TRIPOS>MOLECULE >> JZ4.pdb >> 22 22 1 0 0 >> SMALL >> NO_CHARGES >> >> @<TRIPOS>ATOM >> 1 C4 24.2940 -24.1240 -0.0710 C.3 1 JZ4 0.0000 >> 2 C7 21.5530 -27.2140 -4.1120 C.ar 1 JZ4 0.0000 >> 3 C8 22.0680 -26.7470 -5.3310 C.ar 1 JZ4 0.0000 >> 4 C9 22.6710 -25.5120 -5.4480 C.ar 1 JZ4 0.0000 >> 5 C10 22.7690 -24.7300 -4.2950 C.ar 1 JZ4 0.0000 >> 6 C11 21.6930 -26.4590 -2.9540 C.ar 1 JZ4 0.0000 >> 7 C12 22.2940 -25.1870 -3.0750 C.ar 1 JZ4 0.0000 >> 8 C13 22.4630 -24.4140 -1.8080 C.3 1 JZ4 0.0000 >> 9 C14 23.9250 -24.7040 -1.3940 C.3 1 JZ4 0.0000 >> 10 OAB 23.4120 -23.5360 -4.3420 O.3 1 JZ4 0.0000 >> 11 H7 21.0447 -28.1661 -4.0737 H 1 JZ4 0.0000 >> 12 H8 21.9896 -27.3751 -6.2061 H 1 JZ4 0.0000 >> 13 H9 23.0531 -25.1628 -6.3959 H 1 JZ4 0.0000 >> 14 H11 21.3551 -26.8308 -1.9980 H 1 JZ4 0.0000 >> 15 H132 22.3119 -23.3483 -1.9799 H 1 JZ4 0.0000 >> 16 H133 21.7732 -24.7775 -1.0463 H 1 JZ4 0.0000 >> 17 H142 24.0626 -25.7843 -1.3476 H 1 JZ4 0.0000 >> 18 H143 24.5923 -24.2974 -2.1540 H 1 JZ4 0.0000 >> 19 HAB 22.8219 -22.8428 -4.0372 H 1 JZ4 0.0000 >> 20 H41 25.3323 -24.3661 0.1556 H 1 JZ4 0.0000 >> 21 H42 24.1722 -23.0413 -0.1025 H 1 JZ4 0.0000 >> 22 H43 23.6470 -24.5401 0.7013 H 1 JZ4 0.0000 >> @<TRIPOS>BOND >> 1 1 9 1 >> 2 2 3 ar >> 3 2 6 ar >> 4 3 4 ar >> 5 4 5 ar >> 6 5 7 ar >> 7 5 10 1 >> 8 6 7 ar >> 9 7 8 1 >> 10 8 9 1 >> 11 11 2 1 >> 12 12 3 1 >> 13 13 4 1 >> 14 14 6 1 >> 15 15 8 1 >> 16 16 8 1 >> 17 17 9 1 >> 18 18 9 1 >> 19 19 10 1 >> 20 20 1 1 >> 21 21 1 1 >> 22 22 1 1 >> @<TRIPOS>SUBSTRUCTURE >> 1 JZ4 1 RESIDUE 4 A JZ4 0 ROOT >> >> >> On Fri, Oct 11, 2019 at 6:47 PM Justin Lemkul <jalem...@vt.edu> wrote: >> >>> >>> >>> On 10/11/19 8:59 AM, Suprim Tha wrote: >>> > I could not find out difference in residue names. >>> > The .str file is as below >>> > RESI jz4.pdb 0.000 ! param penalty= 0.900 ; charge penalty= >>> 0.342 >>> >>> The residue name is JZ4, not jz4.pdb - change this and the script will >>> work. >>> >>> -Justin >>> >>> > GROUP ! CHARGE CH_PENALTY >>> > ATOM C4 CG331 -0.271 ! 0.285 >>> > ATOM C7 CG2R61 -0.108 ! 0.000 >>> > ATOM C8 CG2R61 -0.113 ! 0.000 >>> > ATOM C9 CG2R61 -0.109 ! 0.000 >>> > ATOM C10 CG2R61 0.105 ! 0.190 >>> > ATOM C11 CG2R61 -0.115 ! 0.000 >>> > ATOM C12 CG2R61 -0.009 ! 0.232 >>> > ATOM C13 CG321 -0.177 ! 0.342 >>> > ATOM C14 CG321 -0.184 ! 0.045 >>> > ATOM OAB OG311 -0.529 ! 0.190 >>> > ATOM H7 HGR61 0.115 ! 0.000 >>> > ATOM H8 HGR61 0.115 ! 0.000 >>> > ATOM H9 HGR61 0.115 ! 0.000 >>> > ATOM H11 HGR61 0.115 ! 0.000 >>> > ATOM H132 HGA2 0.090 ! 0.000 >>> > ATOM H133 HGA2 0.090 ! 0.000 >>> > ATOM H142 HGA2 0.090 ! 0.000 >>> > ATOM H143 HGA2 0.090 ! 0.000 >>> > ATOM HAB HGP1 0.420 ! 0.000 >>> > ATOM H41 HGA3 0.090 ! 0.000 >>> > ATOM H42 HGA3 0.090 ! 0.000 >>> > ATOM H43 HGA3 0.090 ! 0.000 >>> > BOND C4 C14 >>> > BOND C4 H41 >>> > BOND C4 H42 >>> > BOND C4 H43 >>> > BOND C7 C8 >>> > BOND C7 C11 >>> > BOND C7 H7 >>> > BOND C8 C9 >>> > BOND C8 H8 >>> > BOND C9 C10 >>> > BOND C9 H9 >>> > BOND C10 C12 >>> > BOND C10 OAB >>> > BOND C11 C12 >>> > BOND C11 H11 >>> > BOND C12 C13 >>> > BOND C13 C14 >>> > BOND C13 H132 >>> > BOND C13 H133 >>> > BOND C14 H142 >>> > BOND C14 H143 >>> > BOND OAB HAB >>> > END >>> > read param card flex append >>> > * Parameters generated by analogy by >>> > * CHARMM General Force Field (CGenFF) program version 2.2.0 >>> > * >>> > ! Penalties lower than 10 indicate the analogy is fair; penalties >>> between 10 >>> > ! and 50 mean some basic validation is recommended; penalties higher >>> than >>> > ! 50 indicate poor analogy and mandate extensive >>> validation/optimization. >>> > BONDS >>> > ANGLES >>> > DIHEDRALS >>> > CG321 CG2R61 CG2R61 OG311 2.4000 2 180.00 ! jz4.pdb , from >>> CG311 >>> > CG2R61 CG2R61 OG311, penalty= 0.6 >>> > CG2R61 CG321 CG321 CG331 0.0400 3 0.00 ! jz4.pdb , from >>> CG2R61 >>> > CG321 CG321 CG321, penalty= 0.9 >>> > IMPROPERS >>> > END >>> > RETURN >>> > The .mol2 file is as below >>> > @<TRIPOS>MOLECULE >>> > jz4.pdb >>> > 22 22 1 0 0 >>> > SMALL >>> > NO_CHARGES >>> > >>> > @<TRIPOS>ATOM >>> > 1 C4 24.2940 -24.1240 -0.0710 C.3 1 JZ4 >>> 0.0000 >>> > 2 C7 21.5530 -27.2140 -4.1120 C.ar 1 JZ4 >>> 0.0000 >>> > 3 C8 22.0680 -26.7470 -5.3310 C.ar 1 JZ4 >>> 0.0000 >>> > 4 C9 22.6710 -25.5120 -5.4480 C.ar 1 JZ4 >>> 0.0000 >>> > 5 C10 22.7690 -24.7300 -4.2950 C.ar 1 JZ4 >>> 0.0000 >>> > 6 C11 21.6930 -26.4590 -2.9540 C.ar 1 JZ4 >>> 0.0000 >>> > 7 C12 22.2940 -25.1870 -3.0750 C.ar 1 JZ4 >>> 0.0000 >>> > 8 C13 22.4630 -24.4140 -1.8080 C.3 1 JZ4 >>> 0.0000 >>> > 9 C14 23.9250 -24.7040 -1.3940 C.3 1 JZ4 >>> 0.0000 >>> > 10 OAB 23.4120 -23.5360 -4.3420 O.3 1 JZ4 >>> 0.0000 >>> > 11 H7 21.0447 -28.1661 -4.0737 H 1 JZ4 >>> 0.0000 >>> > 12 H8 21.9896 -27.3751 -6.2061 H 1 JZ4 >>> 0.0000 >>> > 13 H9 23.0531 -25.1628 -6.3959 H 1 JZ4 >>> 0.0000 >>> > 14 H11 21.3551 -26.8308 -1.9980 H 1 JZ4 >>> 0.0000 >>> > 15 H132 22.3119 -23.3483 -1.9799 H 1 JZ4 >>> 0.0000 >>> > 16 H133 21.7732 -24.7775 -1.0463 H 1 JZ4 >>> 0.0000 >>> > 17 H142 24.0626 -25.7843 -1.3476 H 1 JZ4 >>> 0.0000 >>> > 18 H143 24.5923 -24.2974 -2.1540 H 1 JZ4 >>> 0.0000 >>> > 19 HAB 22.8219 -22.8428 -4.0372 H 1 JZ4 >>> 0.0000 >>> > 20 H41 25.3323 -24.3661 0.1556 H 1 JZ4 >>> 0.0000 >>> > 21 H42 24.1722 -23.0413 -0.1025 H 1 JZ4 >>> 0.0000 >>> > 22 H43 23.6470 -24.5401 0.7013 H 1 JZ4 >>> 0.0000 >>> > @<TRIPOS>BOND >>> > 1 1 9 1 >>> > 2 2 3 ar >>> > 3 2 6 ar >>> > 4 3 4 ar >>> > 5 4 5 ar >>> > 6 5 7 ar >>> > 7 5 10 1 >>> > 8 6 7 ar >>> > 9 7 8 1 >>> > 10 8 9 1 >>> > 11 11 2 1 >>> > 12 12 3 1 >>> > 13 13 4 1 >>> > 14 14 6 1 >>> > 15 15 8 1 >>> > 16 16 8 1 >>> > 17 17 9 1 >>> > 18 18 9 1 >>> > 19 19 10 1 >>> > 20 20 1 1 >>> > 21 21 1 1 >>> > 22 22 1 1 >>> > @<TRIPOS>SUBSTRUCTURE >>> > 1 JZ4 1 RESIDUE 4 A JZ4 0 ROOT >>> > >>> > >>> > On Fri, Oct 11, 2019 at 6:38 PM Nidhi singh <tanwar.nid...@gmail.com> >>> wrote: >>> > >>> >> The file is not recognising your .str file. The name must be >>> different in >>> >> your mol2 file and str file. You just need to rectify that. >>> >> >>> >> >>> >> >>> >> On Fri, 11 Oct 2019 at 8:51 PM, Suprim Tha < >>> shrestha.suprim...@gmail.com> >>> >> wrote: >>> >> >>> >>> I was trying gromacs tutorial on molecular dynamics simulation of >>> >>> protein-ligand complex. Everything was going well until the step to >>> >>> convert CHARMM >>> >>> jz4.str file into GROMACS files using the command >>> >>> python cgenff_charmm2gmx_py2.py JZ4 jz4.mol2 jz4.str >>> charmm36-mar2019.ff >>> >>> The error was: >>> >>> Error in atomgroup.py: read_mol2_coor_only: no. of atoms in mol2 >>> (22) and >>> >>> top (0) are unequal >>> >>> Usually this means the specified residue name does not match between >>> str >>> >>> and mol2 files. >>> >>> I have attached the generated str and mol2 files. >>> >>> Please help me find the error. >>> >>> -- >>> >>> 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. >>> >> -- >>> >> Dr. Nidhi >>> >> PhD >>> >> -- >>> >> 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. >>> Assistant Professor >>> Office: 301 Fralin Hall >>> Lab: 303 Engel Hall >>> >>> Virginia Tech Department of Biochemistry >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.thelemkullab.com >>> >>> ================================================== >>> >>> -- >>> 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? 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