[gmx-users] Gromacs tutorial
Suprim Tha
shrestha.suprim123 at gmail.com
Fri Oct 11 15:13:35 CEST 2019
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.suprim123 at 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 <jalemkul at 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.nidhi7 at 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.suprim123 at 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
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>> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> >>> send a mail to gmx-users-request at gromacs.org.
>> >> --
>> >> Dr. Nidhi
>> >> PhD
>> >> --
>> >> Gromacs Users mailing list
>> >>
>> >> * Please search the archive at
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>> >> posting!
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>> >>
>>
>> --
>> ==================================================
>>
>> 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
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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>> Gromacs Users mailing list
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>> posting!
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