[gmx-users] Gromacs tutorial

Suprim Tha shrestha.suprim123 at gmail.com
Fri Oct 11 14:59:18 CEST 2019 

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
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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