AMBER Archive (2009)

Subject: Re: [AMBER] too many missing parameters in frcmod for the prep of my ligand

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Sep 30 2009 - 05:30:32 CDT

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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