[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
>>>>>>
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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
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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

==================================================



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