Dear Amber users,
I am setting up a frcmod file to do the perturbation
imidazole --> nothing in a box of waters.
I get the following error message when I use the
command saveamberparmpert in leap:
*** Proper torsion parameters missing ***
atom names: ND1-CG-CB-HB2
atom types: NB-CC-CT-HC =pert=> DNB-DCC-DCT-DHC
Please add a dummy parameter of multiplicity 2
for the pert types to your parameter set.
- e.g. DNB-DCC-DCT-DHC 1 0.0 0. 2.
I have added the missing parameters but I keep getting
the same errors. Any ideas ?
thanks, alessandra
My frcmod file is the following:
All atom ff for imidazole to nothing perturbation in water.
MASS
DCC 12.01 dummy sp2 aromatic C, 5 memb. ring HIS
DCR 12.01 dummy sp2 arom as CQ but in HIS
DCT 12.01 dummy sp3 aliphatic C
DCW 12.01 dummy sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS)
DH 1.008 dummy H bonded to nitrogen atoms
DHC 1.008 dummy H aliph. bond. to C without electrwd.group
DH4 1.008 dummy H arom. bond. to C with 1 electrwd. group
DH5 1.008 dummy H arom. bond. to C with 2 electrwd. groups
DNA 14.01 dummy sp2 N in 5 memb.ring w/H atom (HIS)
DNB 14.01 dummy sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
CC 12.01 sp2 aromatic C, 5 memb. ring HIS
CR 12.01 sp2 arom as CQ but in HIS
CT 12.01 sp3 aliphatic C
CW 12.01 sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS)
H 1.008 H bonded to nitrogen atoms
HC 1.008 H aliph. bond. to C without electrwd.group
H4 1.008 H arom. bond. to C with 1 electrwd. group
H5 1.008 H arom. bond. to C with 2 electrwd. groups
HW 1.008 H in TIP3P water
NA 14.01 sp2 N in 5 memb.ring w/H atom (HIS)
NB 14.01 sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
OW 16.00 oxygen in TIP3P water
BOND
OW-HW 553.0 0.9572 ! TIP3P water
HW-HW 553.0 1.5136 TIP3P water
CT-HC 340.0 1.090 changed from 331 bsd on NMA nmodes; AA, SUGARS
H -NA 434.0 1.010 JCC,7,(1986),230; GUA,URA,HIS
C*-CW 546.0 1.352 JCC,7,(1986),230; TRP
CC-CT 317.0 1.504 JCC,7,(1986),230; HIS
CC-CW 518.0 1.371 JCC,7,(1986),230; HIS(epsilon)
CC-NB 410.0 1.394 JCC,7,(1986),230; HIS
CR-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes;HIS
CR-NA 477.0 1.343 JCC,7,(1986),230; HIS
CR-NB 488.0 1.335 JCC,7,(1986),230; HIS
CW-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+)
CW-NA 427.0 1.381 JCC,7,(1986),230; HIS,TRP
DCT-DHC 340.0 1.090 changed from 331 bsd on NMA nmodes; AA, SUGARS
DH -DNA 434.0 1.010 JCC,7,(1986),230; GUA,URA,HIS
DC*-DCW 546.0 1.352 JCC,7,(1986),230; TRP
DCC-DCT 317.0 1.504 JCC,7,(1986),230; HIS
DCC-DCW 518.0 1.371 JCC,7,(1986),230; HIS(epsilon)
DCC-DNB 410.0 1.394 JCC,7,(1986),230; HIS
DCR-DH5 367.0 1.080 changed from 340. bsd on C6H6 nmodes;HIS
DCR-DNA 477.0 1.343 JCC,7,(1986),230; HIS
DCR-DNB 488.0 1.335 JCC,7,(1986),230; HIS
DCW-DH4 367.0 1.080 changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+)
DCW-DNA 427.0 1.381 JCC,7,(1986),230; HIS,TRP
ANGL
HW-OW-HW 100. 104.52 TIP3P water
HW-HW-OW 0. 127.74 (found in crystallographic water with 3 bonds)
HC-CT-HC 35.0 109.50
CC-CT-HC 50.0 109.50 AA his changed based on NMA nmodes
CT-CC-NB 70.0 120.00 AA his
CW-CC-NB 70.0 120.00 AA his
CT-CC-CW 70.0 120.00 AA his
H5-CR-NA 35.0 120.00 AA his
H5-CR-NB 35.0 120.00 AA his
NA-CR-NB 70.0 120.00 AA his
CC-CW-H4 35.0 120.00 AA his
CC-CW-NA 70.0 120.00 AA his
H4-CW-NA 35.0 120.00 AA his
C*-CW-H4 35.0 120.00 AA trp
C*-CW-NA 70.0 108.70 AA trp
CT-C*-CW 70.0 125.00 AA trp
CR-NA-CW 70.0 120.00 AA his
CR-NA-H 30.0 120.00 AA his, changed based on NMA nmodes
CW-NA-H 30.0 120.00 AA his, changed based on NMA nmodes
CC-NB-CR 70.0 117.00 AA his
DHC-DCT-DHC 35.0 109.50
DCC-DCT-DHC 50.0 109.50 AA his changed based on NMA nmodes
DCT-DCC-DNB 70.0 120.00 AA his
DCW-DCC-DNB 70.0 120.00 AA his
DCT-DCC-DCW 70.0 120.00 AA his
DH5-DCR-DNA 35.0 120.00 AA his
DH5-DCR-DNB 35.0 120.00 AA his
DNA-DCR-DNB 70.0 120.00 AA his
DCC-DCW-DH4 35.0 120.00 AA his
DCC-DCW-DNA 70.0 120.00 AA his
DH4-DCW-DNA 35.0 120.00 AA his
DC*-DCW-DH4 35.0 120.00 AA trp
DC*-DCW-DNA 70.0 108.70 AA trp
DCT-DC*-DCW 70.0 125.00 AA trp
DCR-DNA-DCW 70.0 120.00 AA his
DCR-DNA-DH 30.0 120.00 AA his, changed based on NMA nmodes
DCW-DNA-DH 30.0 120.00 AA his, changed based on NMA nmodes
DCC-DNB-DCR 70.0 117.00 AA his
DIHE
X -CC-CT-X 6 0.00 0.0 2. JCC,7,(1986),230
X -CC-CW-X 4 21.50 180.0 2. intrpol.bsd.on C6H6
X -CC-NB-X 2 4.80 180.0 2. JCC,7,(1986),230
X -CR-NA-X 4 9.30 180.0 2. JCC,7,(1986),230
X -CR-NB-X 2 10.00 180.0 2. JCC,7,(1986),230
X -CW-NA-X 4 6.00 180.0 2. JCC,7,(1986),230
DNB-DCC-DCT-DHC 1 0.0 0. 2.
DNB-DCC-DCT-DHC 1 0.0 0. 2.
DNB-DCC-DCT-DHC 1 0.0 0. 2.
DCR-DNA-DCW-DCC 1 0.0 0. 2.
DCR-DNB-DCC-DCT 1 0.0 0. 2.
DH5-DCR-DNB-DCC 1 0.0 0. 2.
DNA-DCR-DNB-DCC 1 0.0 0. 2.
DNA-DCW-DCC-DCT 1 0.0 0. 2.
DNA-DCW-DCC-DNB 1 0.0 0. 2.
DH-DNA-DCR-DH5 1 0.0 0. 2.
DH-DNA-DCR-DNB 1 0.0 0. 2.
DH-DNA-DCW-DCC 1 0.0 0. 2.
DCW-DCC-DCT-DHC 1 0.0 0. 2.
DCW-DCC-DCT-DHC 1 0.0 0. 2.
DCW-DCC-DCT-DHC 1 0.0 0. 2.
DCW-DCC-DNB-DCR 1 0.0 0. 2.
DCW-DNA-DCR-DH5 1 0.0 0. 2.
DCW-DNA-DCR-DNB 1 0.0 0. 2.
DH4-DCW-DCC-DCT 1 0.0 0. 2.
DH4-DCW-DCC-DNB 1 0.0 0. 2.
DH4-DCW-DNA-DCR 1 0.0 0. 2.
DH4-DCW-DNA-DH 1 0.0 0. 2.
IMPR
X -X -NA-H 1.0 180. 2. JCC,7,(1986),230
X -X -CW-H4 1.1 180. 2.
X -X -CR-H5 1.1 180. 2.
NA-CW-CC-CT 1.1 180. 2.
DNA-DCW-DCC-DCT 1.1 180. 2.
DCT-DNB-DCC-DCW 0.0 0. 2.
DH5-DNA-DCR-DNB 0.0 0. 2.
DCR-DH-DNA-DCW 0.0 0. 2.
DCC-DNA-DCW-DH4 0.0 0. 2.
NONB
H 0.6000 0.0157 !Ferguson base pair geom.
HC 1.4870 0.0157 OPLS
H4 1.4090 0.0150 Spellmeyer, one electrowithdr. neighbor
H5 1.3590 0.0150 Spellmeyer, two electrowithdr. neighbor
HW 0.0000 0.0000 TIP3P water model
OW 1.7683 0.1520 TIP3P water model
CT 1.9080 0.1094 Spellmeyer
CC 1.9080 0.0860 OPLS
CW 1.9080 0.0860 OPLS
CR 1.9080 0.0860 OPLS
NA 1.8240 0.1700 OPLS
NB 1.8240 0.1700 OPLS
DH 0.6000 0.0157 !Ferguson base pair geom.
DHC 1.4870 0.0157 OPLS
DH4 1.4090 0.0150 Spellmeyer, one electrowithdr. neighbor
DH5 1.3590 0.0150 Spellmeyer, two electrowithdr. neighbor
DCT 1.9080 0.1094 Spellmeyer
DCC 1.9080 0.0860 OPLS
DCW 1.9080 0.0860 OPLS
DCR 1.9080 0.0860 OPLS
DNA 1.8240 0.1700 OPLS
DNB 1.8240 0.1700 OPLS
Received on Fri Nov 03 2000 - 16:23:45 PST
