[gmx-users] Gromacs tutorial
Justin Lemkul
jalemkul at vt.edu
Fri Oct 11 16:07:50 CEST 2019
On 10/11/19 9:44 AM, Suprim Tha wrote:
> 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
What do you mean "did not get any results?" The tutorial system should
run cleanly and will not require modification of any input .mdp files.
Inspect your .log file for errors or anything printed to the terminal.
-Justin
> 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!
>>>>>>>
>>>>>>> * 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-request at 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
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>>>>>> send a mail to gmx-users-request at 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
>>>>
>>>> jalemkul at 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-request at 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
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
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