[gmx-users] charmm36 parameters
Justin A. Lemkul
jalemkul at vt.edu
Mon Jul 2 21:41:32 CEST 2012
On 7/2/12 3:39 PM, Covington, Cody Lance wrote:
> 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?
>
Charges in ffnonbonded.itp are never used for anything.
-Justin
> 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
>
>
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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