[gmx-users] Gromacs tutorial
Suprim Tha
shrestha.suprim123 at gmail.com
Fri Oct 11 15:44:28 CEST 2019
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.suprim123 at 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.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!
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>>> >>> * 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
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
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>>
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