Dear Xueqin Pang,
> 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?
Set the FF atom types in the .mol2 file of your molecules using
capital letters
### LEaP step-1 ###
# Load the FF of your choice in LEaP (leaprc.ff99SB or leaprc.ff03)
xleap -f leaprc.ff99SB
# Load the mol2 file in LEaP
TEST = loadmol2 yourfile.mol2
# save the amber top/crd files you need
saveamberparm TEST TEST.top TEST.crd
The "saveamberparm" command will fail - if missing FF parameters are
found. However, LEaP will provide you the list of the missing FF
parameters. This is only these missing FF parameters you need to
provide in your frcmod file.
In a second LEaP run, you:
### LEaP step-2 ###
# Load the FF of your choice in LEaP (leaprc.ff99SB or leaprc.ff03)
xleap -f leaprc.ff99SB
# load the frcmod files with the missing FF atom types found in the step-1
# (if required)
frcmod = ....
# Load the mol2 file in LEaP
TEST = loadmol2 yourfile.mol2
Solvate... (if required)
addions... (if required)
# save the amber top/crd files you need
saveamberparm TEST TEST.top TEST.crd
regards, Francois
> 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 - 04:00:02 PDT
