[gmx-users] Gromacs tutorial
Justin Lemkul
jalemkul at vt.edu
Fri Oct 11 15:00:27 CEST 2019
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
>>>
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>> --
>> Dr. Nidhi
>> PhD
>> --
>> Gromacs Users mailing list
>>
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--
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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.
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jalemkul at vt.edu | (540) 231-3129
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