Re: [gmx-users] How to reduce the penalty of small molecule from CGenFF

Justin Lemkul Wed, 25 Mar 2020 11:39:20 -0700



On 3/25/20 12:52 PM, Rolly Ng wrote:

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!

Have you read the CGenFF papers? The original 2010 JCC article isbasically a tutorial and review of the parametrization theory.


-Justin


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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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] How to reduce the penalty of small molecule from CGenFF

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