[gmx-users] How to reduce the penalty of small molecule from CGenFF
Justin Lemkul
jalemkul at vt.edu
Wed Mar 25 19:37:57 CET 2020
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 is
basically 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
>
>
>
--
==================================================
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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