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.nid...@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.suprim...@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.
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