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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