Hello, As a part of MD simulation workflow I generated ligand str file using CGenff. The output file had high penalty scores (see below). I am currently performing MM and QM calculations (using ffparam workflow) to re-parameterize the ligand. Is there an alternative way to deal with high penalty scores? The QM and MM calculations are very time consuming and are resulting in different errors.
Any leads would be greatly appreciated.
Thank you in advance.
Regards, Shubhangi
- Toppar stream file generated by
- CHARMM General Force Field (CGenFF) program version 2.5
- For use with CGenFF version 4.6 *
read rtf card append
- Topologies generated by
- CHARMM General Force Field (CGenFF) program version 2.5 * 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 qw3 0.000 ! param penalty= 118.000 ; charge penalty= 64.362 GROUP ! CHARGE CH_PENALTY ATOM C18 CG2R61 -0.106 ! 0.000 ATOM C16 CG2R61 0.074 ! 20.153 ATOM C15 CG2R61 0.005 ! 20.781 ATOM C14 CG2O1 0.319 ! 19.340 ATOM C12 CG3C51 0.007 ! 25.416 ATOM C11 CG2RC0 0.212 ! 16.077 ATOM C10 CG2R61 -0.292 ! 4.088 ATOM C19 CG2R61 0.087 ! 0.000 ATOM C02 CG2O2 0.702 ! 23.363 ATOM C03 CG3C51 -0.169 ! 21.985 ATOM C04 CG3C52 -0.111 ! 21.066 ATOM C05 CG2RC0 0.114 ! 20.490 ATOM C06 CG2R61 0.004 ! 18.170 ATOM C08 CG2R61 -0.153 ! 0.000 ATOM C09 CG2R61 -0.154 ! 0.222 ATOM C21 CG2O6 0.674 ! 8.494 ATOM C23 CG3C31 0.113 ! 64.170 ATOM C24 CG3C31 -0.180 ! 7.029 ATOM C25 CG3C31 -0.180 ! 7.029 ATOM C27 CG2R61 -0.108 ! 0.000 ATOM C28 CG2R61 -0.025 ! 0.000 ATOM N13 NG2S1 -0.256 ! 25.197 ATOM N20 NG2S1 -0.591 ! 5.568 ATOM N22 NG2S1 -0.444 ! 64.362 ATOM O01 OG311 -0.605 ! 9.003 ATOM O07 OG311 -0.563 ! 19.944 ATOM O17 OG311 -0.545 ! 12.465 ATOM O26 OG2D1 -0.483 ! 4.991 ATOM O29 OG2D1 -0.464 ! 4.472 ATOM O30 OG2D1 -0.539 ! 17.764 ATOM H181 HGR61 0.115 ! 0.000 ATOM H121 HGA1 0.090 ! 2.729 ATOM H101 HGR61 0.117 ! 0.207 ATOM H031 HGA1 0.090 ! 2.809 ATOM H042 HGA2 0.090 ! 0.125 ATOM H041 HGA2 0.090 ! 0.125 ATOM H081 HGR61 0.127 ! 0.000 ATOM H091 HGR61 0.127 ! 0.000 ATOM H231 HGA1 0.090 ! 4.871 ATOM H242 HGA2 0.090 ! 2.500 ATOM H241 HGA2 0.090 ! 2.500 ATOM H251 HGA2 0.090 ! 2.500 ATOM H252 HGA2 0.090 ! 2.500 ATOM H271 HGR61 0.115 ! 0.000 ATOM H281 HGR61 0.115 ! 0.000 ATOM H131 HGP1 0.292 ! 6.807 ATOM H201 HGP1 0.295 ! 0.000 ATOM H221 HGP1 0.262 ! 6.220 ATOM H071 HGP1 0.432 ! 0.000 ATOM H171 HGP1 0.420 ! 0.000 ATOM H HGP1 0.430 ! 5.119
