Dear gmx-Users I have downloaded the charmm36 force field for the gromacs website and upon inspection of ffnonbonded.itp found several charges listed as 0.00 with the comment " partial charge def not found" for several atomtypes I am using. Are these charges not used in charmm36?
Thank You in Advance Cody Covington Below is the file ffnonbonded.itp [atomtypes] section ; ; Added new and changed old atomtypes and pairtypes (OSL, OSLP, HBL and CCL) - Thomas Pigot July 2010 ; [ atomtypes ] ;name at.num mass charge ptype sigma epsilon C 6 12.01100 0.51 A 0.356359487256 0.46024 CA 6 12.01100 -0.115 A 0.355005321205 0.29288 CC 6 12.01100 0.62 A 0.356359487256 0.29288 CD 6 12.01100 0.000 A 0.356359487256 0.29288 ; partial charge def not found CE1 6 12.01100 0.000 A 0.372395664183 0.284512 ; partial charge def not found CE2 6 12.01100 0.000 A 0.370613866746 0.267776 ; partial charge def not found CM 6 12.01100 0.000 A 0.374177461619 0.46024 ; partial charge def not found CP1 6 12.01100 0.02 A 0.405358916754 0.08368 CP2 6 12.01100 -0.18 A 0.387540942391 0.23012 CP3 6 12.01100 0.00 A 0.387540942391 0.23012 CPA 6 12.01100 0.000 A 0.320723538531 0.37656 ; partial charge def not found CPB 6 12.01100 0.000 A 0.320723538531 0.37656 ; partial charge def not found CPH1 6 12.01100 0.19 A 0.320723538531 0.2092 CPH2 6 12.01100 0.32 A 0.320723538531 0.2092 CPM 6 12.01100 0.000 A 0.320723538531 0.37656 ; partial charge def not found CPT 6 12.01100 -0.02 A 0.320723538531 0.37656 CS 6 12.01100 0.000 A 0.391995435982 0.46024 ; partial charge def not found CST 6 12.01100 0.000 A 0.278494939291 0.242672 ; partial charge def not found CT1 6 12.01100 0.07 A 0.405358916754 0.08368 CT2 6 12.01100 -0.18 A 0.387540942391 0.23012 CT3 6 12.01100 -0.11 A 0.367050271874 0.33472 CY 6 12.01100 -0.03 A 0.355005321205 0.29288 CT 6 12.01100 0.000 A 0.405358916754 0.08368 ; partial charge def not found CT1x 6 12.01100 0.000 A 0.405358916754 0.08368 ; partial charge def not found CT2x 6 12.01100 0.000 A 0.358141284692 0.234304 ; partial charge def not found CT3x 6 12.01100 0.000 A 0.363486677001 0.326352 ; partial charge def not found H 1 1.008000 0.31 A 0.0400013524445 0.192464 HA 1 1.008000 0.09 A 0.235197261589 0.092048 HE1 1 1.008000 0.000 A 0.222724679535 0.129704 ; partial charge def not found HE2 1 1.008000 0.000 A 0.224506476971 0.108784 ; partial charge def not found HB 1 1.008000 0.09 A 0.235197261589 0.092048 HC 1 1.008000 0.33 A 0.0400013524445 0.192464 HP 1 1.008000 0.115 A 0.242003727796 0.12552 HR1 1 1.008000 0.13 A 0.160361769265 0.192464 HR2 1 1.008000 0.18 A 0.12472582054 0.192464 HR3 1 1.008000 0.09 A 0.261567863646 0.0326352 HS 1 1.008000 0.16 A 0.0801808846326 0.4184 #ifdef HEAVY_H HT 1 4.032 0.417 A 0.0400013524445 0.192464 ; CHARMM TIP3p H #else HT 1 1.008000 0.417 A 0.0400013524445 0.192464 #endif HA1 1 1.008000 0.000 A 0.235197261589 0.092048 ; partial charge def not found HA2 1 1.008000 0.000 A 0.238760856462 0.117152 ; partial charge def not found HA3 1 1.008000 0.000 A 0.238760856462 0.100416 ; partial charge def not found N 7 14.00700 -0.29 A 0.329632525712 0.8368 NC2 7 14.00700 -0.80 A 0.329632525712 0.8368 NH1 7 14.00700 -0.47 A 0.329632525712 0.8368 NH2 7 14.00700 -0.62 A 0.329632525712 0.8368 NH3 7 14.00700 -0.30 A 0.329632525712 0.8368 NP 7 14.00700 0.000 A 0.329632525712 0.8368 ; partial charge def not found NPH 7 14.00700 0.000 A 0.329632525712 0.8368 ; partial charge def not found NR1 7 14.00700 -0.36 A 0.329632525712 0.8368 NR2 7 14.00700 -0.70 A 0.329632525712 0.8368 NR3 7 14.00700 -0.51 A 0.329632525712 0.8368 NY 7 14.00700 -0.61 A 0.329632525712 0.8368 O 8 15.999400 -0.51 A 0.302905564168 0.50208 OB 8 15.999400 0.000 A 0.302905564168 0.50208 ; partial charge def not found OC 8 15.999400 -0.76 A 0.302905564168 0.50208 OH1 8 15.999400 -0.54 A 0.315378146222 0.6363864 OM 8 15.999400 0.000 A 0.302905564168 0.50208 ; partial charge def not found OS 8 15.999400 0.000 A 0.315378146222 0.6363864 ; partial charge def not found OST 8 15.999400 0.000 A 0.301480126219 0.69036 ; partial charge def not found OT 8 15.999400 -0.834 A 0.315057422683 0.6363864 #ifdef HEAVY_H OT 8 9.951400 -0.834 A 0.315057422683 0.6363864 ; CHARMM TIP3p O #endif S 16 32.060000 -0.09 A 0.356359487256 1.8828 SM 16 32.060000 0.000 A 0.351904993665 1.58992 ; partial charge def not found SS 16 32.060000 0.000 A 0.391995435982 1.96648 ; partial charge def not found SOD 11 22.989770 1.00 A 0.242992625373 0.1962296 POT 19 39.102000 1.00 A 0.314264522824 0.364008 CLA 17 35.450000 -1.00 A 0.404468018036 0.6276 CAL 20 40.080000 2.00 A 0.24357170954 0.50208 MG 12 24.305000 2.00 A 0.211142996199 0.06276 CES 55 132.900000 1.00 A 0.374177461619 0.79496 ZN 30 65.370000 2.00 A 0.194215920555 1.046 FE 26 55.84700 0.000 A 0.115816833358 0.0 ; partial charge def not found HE 2 4.00260 0.000 A 0.26370602057 0.08899368 ; partial charge def not found NE 10 20.17970 0.000 A 0.272615007751 0.359824 ; partial charge def not found CLAL 17 35.450000 0.000 A 0.340002586791 0.12552 ; partial charge def not found DUM 1 1.008000 0.000 A 0.0 0.0 ; partial charge def not found CAP 6 12.01100 0.000 A 0.355005321205 0.29288 ; partial charge def not found FA 9 18.99800 0.000 A 0.302905564168 0.50208 ; partial charge def not found CN 6 12.01100 0.000 A 0.311814551349 0.8368 ; partial charge def not found NC 7 14.00700 0.000 A 0.329632525712 2.5104 ; partial charge def not found OCA 8 15.999400 0.000 A 0.302905564168 0.50208 ; partial charge def not found COA 6 12.01100 0.000 A 0.356359487256 0.46024 ; partial charge def not found CF1 6 12.01100 0.000 A 0.338541512893 0.25104 ; partial charge def not found CF2 6 12.01100 0.000 A 0.365268474438 0.175728 ; partial charge def not found CF3 6 12.01100 0.000 A 0.409813410345 0.08368 ; partial charge def not found HF1 1 1.008000 0.000 A 0.235197261589 0.117152 ; partial charge def not found HF2 1 1.008000 0.000 A 0.231633666716 0.12552 ; partial charge def not found F1 9 18.99800 0.000 A 0.290432982114 0.56484 ; partial charge def not found F2 9 18.99800 0.000 A 0.290432982114 0.43932 ; partial charge def not found F3 9 18.99800 0.000 A 0.285087589805 0.405848 ; partial charge def not found C3 6 12.01100 0.000 A 0.405358916754 0.08368 ; partial charge def not found CC1A 6 12.01100 0.000 A 0.372395664183 0.284512 ; partial charge def not found CC1B 6 12.01100 0.000 A 0.372395664183 0.284512 ; partial charge def not found CC2 6 12.01100 0.000 A 0.370613866746 0.267776 ; partial charge def not found NS1 7 14.00700 0.000 A 0.329632525712 0.8368 ; partial charge def not found NS2 7 14.00700 0.000 A 0.329632525712 0.8368 ; partial charge def not found HOL 1 1.008000 0.43 A 0.0400013524445 0.192464 HAL1 1 1.008000 0.09 A 0.235197261589 0.092048 HAL2 1 1.008000 0.09 A 0.238760856462 0.117152 HAL3 1 1.008000 0.09 A 0.238760856462 0.100416 HCL 1 1.008000 0.33 A 0.0400013524445 0.192464 HL 1 1.008000 0.25 A 0.12472582054 0.192464 HEL1 1 1.008000 0.15 A 0.222724679535 0.129704 HEL2 1 1.008000 0.000 A 0.224506476971 0.108784 ; partial charge def not found HBL 1 1.008000 0.10 A 0.235197261589 0.092048 ; Not in C27 CCL 6 12.01100 0.34 A 0.356359487256 0.29288 ; Not in C27 CL 6 12.01100 0.90 A 0.356359487256 0.29288 CTL1 6 12.01100 0.14 A 0.405358916754 0.08368 CTL2 6 12.01100 -0.18 A 0.358141284692 0.234304 CTL3 6 12.01100 -0.27 A 0.363486677001 0.326352 CTL5 6 12.01100 -0.35 A 0.367050271874 0.33472 CEL1 6 12.01100 -0.15 A 0.372395664183 0.284512 CEL2 6 12.01100 0.000 A 0.370613866746 0.267776 ; partial charge def not found OBL 8 15.999400 -0.52 A 0.302905564168 0.50208 OCL 8 15.999400 -0.76 A 0.302905564168 0.50208 O2L 8 15.999400 -0.78 A 0.302905564168 0.50208 OHL 8 15.999400 -0.66 A 0.315378146222 0.6363864 OSL 8 15.999400 -0.49 A 0.293996576986 0.4184 ; Different to C27 OSLP 8 15.999400 -0.57 A 0.293996576986 0.4184 ; Not in C27 NH3L 7 14.00700 -0.30 A 0.329632525712 0.8368 NTL 7 14.00700 -0.60 A 0.329632525712 0.8368 SL 16 32.060000 1.33 A 0.374177461619 1.96648 PL 15 30.974000 1.50 A 0.3830864488 2.44764 ; The following atom types are NOT part of the CHARMM distribution ; atomtypes for additional water models #ifdef HEAVY_H OWT3 8 9.951400 -0.834 A 3.15058e-01 6.36386e-01 ; TIP3p O HWT3 1 4.032000 0.417 A 0.0 0.0 ; TIP3p H OWT4 8 9.951400 0.0 A 3.15365e-01 6.48520e-01 ; TIP4p O HWT4 1 4.032000 0.52 A 0.0 0.0 ; TIP4p H MWT4 0 0.000000 -1.04 A 0.0 0.0 ; TIP4p vsite OWT5 8 9.951400 0.0 A 3.12000e-01 6.69440e-01 ; TIP5p O HWT5 1 4.032000 0.241 A 0.0 0.0 ; TIP5p H MWT5 0 0.000000 -0.241 A 0.0 0.0 ; TIP5p vsite OW 8 9.951400 -0.82 A 3.16557e-01 6.50194e-01 ; SPC 0 HW 1 4.032000 0.41 A 0.0 0.0; SPC H #else OWT3 8 15.999400 -0.834 A 3.15058e-01 6.36386e-01 ; TIP3p O HWT3 1 1.008000 0.417 A 0.0 0.0 ; TIP3p H OWT4 8 15.999400 0.0 A 3.15365e-01 6.48520e-01 ; TIP4p O HWT4 1 1.008000 0.52 A 0.0 0.0 ; TIP4p H MWT4 0 0.000000 -1.04 A 0.0 0.0 ; TIP4p vsite OWT5 8 15.999400 0.0 A 3.12000e-01 6.69440e-01 ; TIP5p O HWT5 1 1.008000 0.241 A 0.0 0.0 ; TIP5p H MWT5 0 0.000000 -0.241 A 0.0 0.0 ; TIP5p vsite OW 8 15.999400 -0.82 A 3.16557e-01 6.50194e-01 ; SPC O HW 1 1.008000 0.41 A 0.0 0.0 ; SPC H #endif ; special dummy-type particles MNH3 0 0.000000 0.00 A 0.0 0.0 MNH2 0 0.000000 0.00 A 0.0 0.0 MCH3 0 0.000000 0.00 A 0.0 0.0 MCH3S 0 0.000000 0.00 A 0.0 0.0 ; Ions and noble gases (useful for tutorials) Cu2+ 29 63.54600 2.00 A 2.08470e-01 4.76976e+00 Ar 18 39.94800 0.00 A 3.41000e-01 2.74580e-02 ; Added by DvdS 05/2005 copied from GROMACS force field. SI 14 28.08000 0.00 A 3.38550e-01 2.44704e+00 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists