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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