[gmx-users] How to reduce the penalty of small molecule from CGenFF
Rolly Ng
rollyng at gmail.com
Wed Mar 25 17:52:38 CET 2020
Dear Gromacs Users,
I am new to Gromacs and I followed the Protein-Ligand tutorial on the
following webpage,
http://www.mdtutorials.com/gmx/complex/02_topology.html
It works for the example JZ4 but as I changed to another molecule, the str
file produced by the CGenFF server states very high penalty 84.5
Please have a look at my mol2 input and str output below. Your advises are
much appreciated!
Thank you,
Rolly
@<TRIPOS>MOLECULE
MF8
20 19 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 N08 19.3800 -17.4900 12.2190 N.pl3 1 MF8 -0.2888
2 C07 19.5160 -18.4740 11.4320 C.cat 1 MF8 0.3855
3 N06 20.0120 -18.2750 10.1980 N.pl3 1 MF8 -0.1861
4 N09 19.1990 -19.7060 11.8570 N.pl3 1 MF8 -0.1293
5 C01 18.6460 -20.7310 8.7020 C.3 1 MF8 0.0558
6 N02 19.3290 -19.4990 8.3110 N.pl3 1 MF8 -0.2675
7 N05 18.6660 -17.3520 8.6680 N.pl3 1 MF8 -0.1291
8 C04 19.3130 -18.3670 9.0550 C.cat 1 MF8 0.3896
9 C03 20.0370 -19.6170 7.0360 C.3 1 MF8 0.0558
10 H 19.6101 -16.5820 11.9161 H 1 MF8 0.2547
11 H 19.0443 -17.6336 13.1333 H 1 MF8 0.2547
12 H 20.9660 -18.0428 10.1266 H 1 MF8 0.2707
13 H 19.3013 -20.4766 11.2529 H 1 MF8 0.3062
14 H 18.8055 -21.4799 7.9546 H 1 MF8 0.0619
15 H 17.5973 -20.5420 8.7994 H 1 MF8 0.0619
16 H 19.0353 -21.0729 9.6382 H 1 MF8 0.0619
17 H 18.1443 -17.3894 7.8339 H 1 MF8 0.3062
18 H 19.9010 -20.6026 6.6424 H 1 MF8 0.0619
19 H 21.0802 -19.4349 7.1891 H 1 MF8 0.0619
20 H 19.6476 -18.8997 6.3441 H 1 MF8 0.0619
@<TRIPOS>BOND
1 1 2 1
2 1 10 1
3 1 11 1
4 2 3 1
5 2 4 2
6 3 8 1
7 3 12 1
8 4 13 1
9 5 6 1
10 5 14 1
11 5 15 1
12 5 16 1
13 6 9 1
14 6 8 1
15 7 8 2
16 7 17 1
17 9 18 1
18 9 19 1
19 9 20 1
* Toppar stream file generated by
* CHARMM General Force Field (CGenFF) program version 1.0.0
* For use with CGenFF version 3.0.1
*
read rtf card append
* Topologies generated by
* CHARMM General Force Field (CGenFF) program version 1.0.0
*
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 MF8 0.000 ! param penalty= 84.500 ; charge penalty= 12.315
GROUP ! CHARGE CH_PENALTY
ATOM N08 NG321 -0.603 ! 2.500
ATOM C07 CG2N1 0.547 ! 5.000
ATOM N06 NG311 -0.430 ! 6.533
ATOM N09 NG2D1 -0.907 ! 2.500
ATOM C01 CG331 -0.141 ! 9.593
ATOM N02 NG301 -0.371 ! 12.315
ATOM N05 NG2D1 -0.861 ! 4.101
ATOM C04 CG2N1 0.609 ! 10.954
ATOM C03 CG331 -0.141 ! 9.593
ATOM H1 HGPAM2 0.330 ! 0.000
ATOM H2 HGPAM2 0.330 ! 0.000
ATOM H3 HGPAM1 0.360 ! 0.090
ATOM H4 HGP1 0.369 ! 0.000
ATOM H5 HGA3 0.090 ! 2.518
ATOM H6 HGA3 0.090 ! 2.518
ATOM H7 HGA3 0.090 ! 2.518
ATOM H8 HGP1 0.369 ! 0.030
ATOM H9 HGA3 0.090 ! 2.518
ATOM H10 HGA3 0.090 ! 2.518
ATOM H11 HGA3 0.090 ! 2.518
BOND N08 C07
BOND N08 H1
BOND N08 H2
BOND C07 N06
BOND C07 N09
BOND N06 C04
BOND N06 H3
BOND N09 H4
BOND C01 N02
BOND C01 H5
BOND C01 H6
BOND C01 H7
BOND N02 C03
BOND N02 C04
BOND N05 C04
BOND N05 H8
BOND C03 H9
BOND C03 H10
BOND C03 H11
IMPR C07 N09 N06 N08
IMPR C04 N05 N02 N06
END
read param card flex append
* Parameters generated by analogy by
* CHARMM General Force Field (CGenFF) program version 1.0.0
*
! 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
CG2N1 NG301 500.00 1.4400 ! MF8 , from CG2N1 NG311, penalty= 5
CG331 NG301 255.00 1.4630 ! MF8 , from CG331 NG311, penalty= 5
ANGLES
NG2D1 CG2N1 NG301 50.00 125.00 ! MF8 , from NG2D1 CG2N1 NG311,
penalty= 0.6
NG301 CG2N1 NG311 50.00 113.00 ! MF8 , from NG311 CG2N1 NG321,
penalty= 1.8
NG301 CG331 HGA3 30.50 109.70 50.00 2.14000 ! MF8 , from NG311
CG331 HGA3, penalty= 0.6
CG2N1 NG301 CG331 43.00 106.00 ! MF8 , from CG2N1 NG311 CG331,
penalty= 5
CG331 NG301 CG331 53.00 110.90 ! MF8 , from CG3AM0 NG301 CG3AM0,
penalty= 36.6
CG2N1 NG311 CG2N1 40.00 109.00 ! MF8 , from CG2R61 NG311 CG2R61,
penalty= 46
DIHEDRALS
NG301 CG2N1 NG2D1 HGP1 5.2000 2 180.00 ! MF8 , from NG311 CG2N1
NG2D1 HGP1, penalty= 0.6
NG2D1 CG2N1 NG301 CG331 0.5000 2 180.00 ! MF8 , from NG2D1 CG2N1
NG311 CG331, penalty= 5
NG311 CG2N1 NG301 CG331 0.5000 2 180.00 ! MF8 , from NG321 CG2N1
NG311 CG331, penalty= 6.2
NG2D1 CG2N1 NG311 CG2N1 0.5000 2 180.00 ! MF8 , from NG2D1 CG2N1
NG311 CG331, penalty= 69.9
NG301 CG2N1 NG311 CG2N1 0.5000 2 180.00 ! MF8 , from NG321 CG2N1
NG311 CG331, penalty= 71.7
NG301 CG2N1 NG311 HGPAM1 2.8000 2 180.00 ! MF8 , from NG321 CG2N1
NG311 HGPAM1, penalty= 1.8
NG321 CG2N1 NG311 CG2N1 0.5000 2 180.00 ! MF8 , from NG321 CG2N1
NG311 CG331, penalty= 69.9
HGA3 CG331 NG301 CG2N1 0.0000 3 180.00 ! MF8 , from HGA3 CG331
NG311 CG2N1, penalty= 5
HGA3 CG331 NG301 CG331 0.0000 3 180.00 ! MF8 , from HGA2 CG321
NG311 CG2R61, penalty= 84.5
IMPROPERS
CG2N1 NG2D1 NG301 NG311 85.0000 0 0.00 ! MF8 , from CG2N1 NG2D1
NG311 NG321, penalty= 1.5
END
RETURN
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