Hello everyone,
I am trying to get a prepi for my ligand using RED, however the parmchk which give out a frcmod listed a lot of missing parameters. I want to know whether this prep can be used in my MD simulation and why it is so?
Thank you so much for your kind help
the frcmod of my ligand as follows:
remark goes here
MASS
CA 12.010 0.360 same as c2
HA 1.008 0.135 same as hc
OH 16.000 0.465 same as oh
HO 1.008 0.135 same as ho
CT 12.010 0.878 same as c3
HC 1.008 0.135 same as hc
H1 1.008 0.135 same as hc
N2 14.010 0.530 same as n3
H 1.008 0.161 same as hn
CB 12.010 0.360 same as c2
NA 14.010 0.530 same as na
CR 12.010 0.360 same as c2
C* 12.010 0.360 same as c2
H4 1.008 0.135 same as ha
OS 16.000 0.465 same as os
BOND
CA-HA 344.30 1.087 same as c2-hc
CA-CA 478.40 1.387 same as ca-ca
CA-OH 425.40 1.333 same as c2-oh
OH-HO 369.60 0.974 same as ho-oh
CA-CT 328.30 1.508 same as c2-c3
CT-HC 337.30 1.092 same as c3-hc
CT-CT 303.10 1.535 same as c3-c3
CT-H1 337.30 1.092 same as c3-hc
CT-N2 320.60 1.470 same as c3-n3
N2-H 394.10 1.018 same as hn-n3
N2-CA 449.00 1.364 same as ca-nh
N2-CB 449.00 1.364 same as cc-nh
N2-CR 449.00 1.364 same as cc-nh
N2-NA 426.70 1.420 same as n3-na
NA-H 406.60 1.011 same as hn-na
NA-CR 411.10 1.391 same as c2-na
CR-C* 418.30 1.429 same as cc-cc
C*-C* 418.30 1.429 same as cc-cc
C*-OS 392.60 1.357 same as c2-os
C*-HA 344.30 1.087 same as c2-hc
C*-CA 411.70 1.434 same as ca-cc
CA-H4 344.30 1.087 same as c2-ha
CA-OS 392.60 1.357 same as c2-os
ANGLE
CA-CA-HA 50.300 119.700 same as c2-c2-hc
CA-CA-CA 67.200 119.970 same as ca-ca-ca
CA-CA-CT 64.300 123.420 same as c2-c2-c3
CA-CA-OH 71.600 122.280 same as c2-c2-oh
CA-OH-HO 49.900 108.980 same as c2-oh-ho
CA-CT-HC 47.000 110.490 same as c2-c3-hc
CA-CT-CT 63.700 110.960 same as c2-c3-c3
CT-CT-H1 46.400 110.050 same as c3-c3-hc
CT-CT-N2 66.200 110.380 same as c3-c3-n3
HC-CT-HC 39.400 108.350 same as hc-c3-hc
HC-CT-CT 46.400 110.050 same as c3-c3-hc
CT-N2-H 47.100 109.920 same as c3-n3-hn
CT-N2-CA 62.820 117.790 Calculated with empirical approach
H1-CT-H1 39.400 108.350 same as hc-c3-hc
H1-CT-N2 49.400 109.800 same as hc-c3-n3
N2-CA-N2 71.400 120.980 same as nh-ca-nh
H -N2-CA 49.100 119.380 same as c2-n3-hn
CA-N2-CA 64.300 127.460 same as ca-nh-ca
CA-N2-CB 66.200 124.680 same as c2-n3-c2
CA-N2-NA 66.760 118.340 Calculated with empirical approach
H -N2-H 41.300 107.130 same as hn-n3-hn
N2-CB-N2 72.900 115.960 same as nh-cc-nh
.....
DIHE
CA-CA-CA-OH 1 6.650 180.000 2.000 same as X -c2-c2-X
CA-CA-CA-CA 1 3.625 180.000 2.000 same as X -ca-ca-X
CA-CA-CA-HA 1 6.650 180.000 2.000 same as X -c2-c2-X
CA-CA-CT-HC 1 0.380 180.000 -3.000 same as hc-c3-c2-c2
CA-CA-CT-HC 1 1.150 0.000 1.000 same as hc-c3-c2-c2
CA-CA-CT-CT 1 0.000 0.000 2.000 same as X -c2-c3-X
HA-CA-CA-HA 1 6.650 180.000 2.000 same as X -c2-c2-X
HA-CA-CA-CT 1 6.650 180.000 2.000 same as X -c2-c2-X
CA-CA-CA-CT 1 6.650 180.000 2.000 same as X -c2-c2-X
CA-CA-OH-HO 1 1.050 180.000 2.000 same as X -c2-oh-X
HA-CA-CA-OH 1 6.650 180.000 2.000 same as X -c2-c2-X
CA-CT-CT-H1 1 0.156 0.000 3.000 same as X -c3-c3-X
CA-CT-CT-N2 1 0.156 0.000 3.000 same as X -c3-c3-X
CT-CT-N2-H 1 0.300 0.000 3.000 same as X -c3-n3-X
CT-CT-N2-CA 1 0.300 0.000 3.000 same as X -c3-n3-X
HC-CT-CT-H1 1 0.150 0.000 3.000 same as hc-c3-c3-hc
....
IMPROPER
CA-CA-CA-HA 1.1 180.0 2.0 Using default value
CA-CA-CA-OH 1.1 180.0 2.0 Using default value
CA-CA-CA-CT 1.1 180.0 2.0 Using default value
CA-CT-N2-H 1.1 180.0 2.0 Using default value
N2-N2-CA-N2 1.1 180.0 2.0 Using default value
CA-CA-N2-H 1.1 180.0 2.0 Using default value
CA-H -N2-H 1.1 180.0 2.0 Using default value
CA-CB-N2-H 1.1 180.0 2.0 Using default value
....
NONBON
CA 1.9080 0.0860 same as ca
HA 1.4870 0.0157 same as hc
OH 1.7210 0.2104 same as oh
HO 0.0000 0.0000 same as ho
CT 1.9080 0.1094 same as c3
HC 1.4870 0.0157 same as hc
H1 1.4870 0.0157 same as hc
N2 1.8240 0.1700 same as nh
H 0.6000 0.0157 same as hn
CB 1.9080 0.0860 same as cc
NA 1.8240 0.1700 same as na
CR 1.9080 0.0860 same as cc
C* 1.9080 0.0860 same as cc
H4 1.4870 0.0157 same as hc
OS 1.6837 0.1700 same as os
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Received on Wed Sep 30 2009 - 02:30:03 PDT
