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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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