> You likely have zero Lennard-Jones parameters on the proton bound to
> > oxygen.
> >
> > How can I add Lennard-Jones parameter for the proton?
>
> You'll need to define a new atom type for hydrogen bound to the side chain
> oxygen, and give it LJ parameters in the parm.dat (or frcmod) file.
>
I define atom types using this command line:
>parmchk -i $mol2File -f mol2 -o $frcMod
and it will produce following frcmod file:
remark goes here
MASS
N3 14.010 0.530 same as n4
CT 12.010 0.878 same as c3
C 12.010 0.616 same as c
O 16.000 0.434 same as o
H 1.008 0.161 same as hn
HP 1.008 0.135 same as hc
HC 1.008 0.135 same as hc
N 14.010 0.530 same as n
H1 1.008 0.135 same as hc
CM 12.010 0.360 same as c2
OS 16.000 0.465 same as os
NB 14.010 0.530 same as n2
OH 16.000 0.465 same as oh
HO 1.008 0.135 same as ho
BOND
N3-CT 293.60 1.499 same as c3-n4
N3-H 369.00 1.033 same as hn-n4
CT-C 328.30 1.508 same as c -c3
CT-HP 337.30 1.092 same as c3-hc
CT-CT 303.10 1.535 same as c3-c3
C -O 648.00 1.214 same as c -o
C -N 478.20 1.345 same as c -n
CT-HC 337.30 1.092 same as c3-hc
N -CT 330.60 1.460 same as c3-n
N -H 410.20 1.009 same as hn-n
CT-H1 337.30 1.092 same as c3-hc
CT-CM 328.30 1.508 same as c2-c3
CM-OS 392.60 1.357 same as c2-os
CM-NB 431.60 1.376 same as cc-nc
OS-C 411.30 1.343 same as c -os
NB-CT 313.80 1.477 same as c3-n2
C -OH 466.40 1.306 same as c -oh
OH-HO 369.60 0.974 same as ho-oh
ANGLE
N3-CT-C 65.070 114.210 same as c -c3-n4
N3-CT-HP 49.010 107.900 same as hc-c3-n4
N3-CT-CT 64.450 114.320 same as c3-c3-n4
CT-N3-H 46.190 110.110 same as c3-n4-hn
CT-C -O 68.030 123.110 same as c3-c -o
CT-C -N 67.860 115.150 same as c3-c -n
CT-CT-HC 46.370 110.050 same as c3-c3-hc
C -CT-HP 47.200 109.680 same as c -c3-hc
C -CT-CT 63.790 110.530 same as c -c3-c3
C -N -CT 63.920 121.350 same as c -n -c3
C -N -H 49.210 118.460 same as c -n -hn
O -C -N 75.830 122.030 same as n -c -o
H -N3-H 40.520 108.110 same as hn-n4-hn
HP-CT-CT 46.370 110.050 same as c3-c3-hc
HC-CT-HC 39.430 108.350 same as hc-c3-hc
N -CT-C 66.670 111.560 same as c -c3-n
N -CT-H1 49.780 109.500 same as hc-c3-n
N -CT-CT 65.850 112.130 same as c3-c3-n
CT-N -H 46.040 116.780 same as c3-n -hn
C -CT-H1 47.200 109.680 same as c -c3-hc
H1-CT-CT 46.370 110.050 same as c3-c3-hc
N -CT-CM 66.730 111.380 same as c2-c3-n
CT-CM-OS 68.770 112.690 same as c3-c2-os
CT-CM-NB 66.470 123.520 same as c3-c2-n2
CM-CT-H1 47.030 110.490 same as c2-c3-hc
CM-CT-CT 63.530 111.440 same as c2-c3-c3
CM-OS-C 64.910 118.020 same as c -os-c2
CM-NB-CT 66.130 115.300 same as c2-n2-c3
OS-CM-NB 74.320 119.820 same as n2-c2-os
OS-C -CT 69.260 111.960 same as c3-c -os
OS-C -O 75.930 123.330 same as o -c -os
NB-CT-C 66.920 109.550 same as c -c3-n2
NB-CT-H1 49.290 109.500 same as hc-c3-n2
NB-CT-CT 66.400 109.160 same as c3-c3-n2
CT-C -OH 69.840 112.200 same as c3-c -oh
C -CT-HC 47.200 109.680 same as c -c3-hc
C -OH-HO 51.190 107.370 same as c -oh-ho
OH-C -O 77.380 122.880 same as o -c -oh
DIHE
N3-CT-C -O 1 0.000 180.000 2.000 same as X -c
-c3-X
N3-CT-C -N 1 0.000 180.000 2.000 same as X -c
-c3-X
N3-CT-CT-HC 1 0.156 0.000 3.000 same as X
-c3-c3-X
CT-C -N -CT 1 2.500 180.000 2.000 same as X -c -n
-X
CT-C -N -H 1 2.500 180.000 2.000 same as X -c -n
-X
C -CT-N3-H 1 0.156 0.000 3.000 same as X
-c3-n4-X
C -CT-CT-HC 1 0.156 0.000 3.000 same as X
-c3-c3-X
C -N -CT-C 1 0.850 180.000 -2.000 same as c -n
-c3-c
C -N -CT-C 1 0.800 0.000 1.000 same as c -n
-c3-c
C -N -CT-H1 1 0.000 0.000 2.000 same as X -c3-n
-X
C -N -CT-CT 1 0.500 180.000 -4.000 same as c3-c3-n
-c
C -N -CT-CT 1 0.150 180.000 -3.000 same as c3-c3-n
-c
C -N -CT-CT 1 0.530 0.000 1.000 same as c3-c3-n
-c
O -C -CT-HP 1 0.800 0.000 -1.000 same as hc-c3-c
-o
O -C -CT-HP 1 0.080 180.000 3.000 same as hc-c3-c
-o
O -C -CT-CT 1 0.000 180.000 2.000 same as X -c
-c3-X
O -C -N -CT 1 2.500 180.000 2.000 same as X -c -n
-X
O -C -N -H 1 2.500 180.000 -2.000 same as hn-n -c
-o
O -C -N -H 1 2.000 0.000 1.000 same as hn-n -c
-o
H -N3-CT-HP 1 0.156 0.000 3.000 same as X
-c3-n4-X
H -N3-CT-CT 1 0.156 0.000 3.000 same as X
-c3-n4-X
HP-CT-C -N 1 0.000 180.000 2.000 same as X -c
-c3-X
HP-CT-CT-HC 1 0.150 0.000 3.000 same as
hc-c3-c3-hc
CT-CT-C -N 1 0.100 0.000 -4.000 same as c3-c3-c
-n
CT-CT-C -N 1 0.070 0.000 2.000 same as c3-c3-c
-n
N -CT-C -O 1 0.000 180.000 2.000 same as X -c
-c3-X
N -CT-C -N 1 1.700 180.000 -1.000 same as n -c3-c
-n
N -CT-C -N 1 2.000 180.000 2.000 same as n -c3-c
-n
N -CT-CT-HC 1 0.156 0.000 3.000 same as X
-c3-c3-X
C -CT-N -H 1 0.000 0.000 2.000 same as X -c3-n
-X
O -C -CT-H1 1 0.800 0.000 -1.000 same as hc-c3-c
-o
O -C -CT-H1 1 0.080 180.000 3.000 same as hc-c3-c
-o
H -N -CT-H1 1 0.000 0.000 2.000 same as X -c3-n
-X
H -N -CT-CT 1 0.000 0.000 2.000 same as X -c3-n
-X
H1-CT-C -N 1 0.000 180.000 2.000 same as X -c
-c3-X
H1-CT-CT-HC 1 0.150 0.000 3.000 same as
hc-c3-c3-hc
C -N -CT-CM 1 0.000 0.000 2.000 same as X -c3-n
-X
N -CT-CM-OS 1 0.000 0.000 2.000 same as X
-c2-c3-X
N -CT-CM-NB 1 0.000 0.000 2.000 same as X
-c2-c3-X
CT-CM-OS-C 1 1.050 180.000 2.000 same as X
-c2-os-X
CT-CM-NB-CT 1 4.150 180.000 2.000 same as X
-c2-n2-X
CM-CT-N -H 1 0.000 0.000 2.000 same as X -c3-n
-X
CM-CT-CT-HC 1 0.156 0.000 3.000 same as X
-c3-c3-X
CM-OS-C -CT 1 2.700 180.000 2.000 same as X -c
-os-X
CM-OS-C -O 1 2.700 180.000 2.000 same as X -c
-os-X
CM-NB-CT-C 1 0.000 0.000 3.000 same as X
-c3-n2-X
CM-NB-CT-H1 1 0.000 0.000 3.000 same as X
-c3-n2-X
CM-NB-CT-CT 1 0.000 0.000 3.000 same as X
-c3-n2-X
OS-CM-CT-H1 1 0.000 0.000 2.000 same as X
-c2-c3-X
OS-CM-CT-CT 1 0.000 0.000 2.000 same as X
-c2-c3-X
OS-CM-NB-CT 1 4.150 180.000 2.000 same as X
-c2-n2-X
OS-C -CT-NB 1 0.000 180.000 2.000 same as X -c
-c3-X
OS-C -CT-H1 1 0.000 180.000 2.000 same as X -c
-c3-X
OS-C -CT-CT 1 0.000 180.000 2.000 same as X -c
-c3-X
H1-CT-CM-NB 1 0.000 0.000 2.000 same as X
-c2-c3-X
CT-CT-CM-NB 1 0.000 0.000 2.000 same as X
-c2-c3-X
NB-CM-OS-C 1 1.050 180.000 2.000 same as X
-c2-os-X
NB-CT-C -O 1 0.000 180.000 2.000 same as X -c
-c3-X
NB-CT-CT-C 1 0.156 0.000 3.000 same as X
-c3-c3-X
NB-CT-CT-HC 1 0.156 0.000 3.000 same as X
-c3-c3-X
CT-CT-C -OH 1 0.000 180.000 2.000 same as X -c
-c3-X
C -CT-CT-C 1 0.156 0.000 3.000 same as X
-c3-c3-X
H1-CT-CT-C 1 0.156 0.000 3.000 same as X
-c3-c3-X
CT-C -OH-HO 1 2.300 180.000 2.000 same as X -c
-oh-X
HC-CT-C -OH 1 0.000 180.000 2.000 same as X -c
-c3-X
HC-CT-C -O 1 0.800 0.000 -1.000 same as hc-c3-c
-o
HC-CT-C -O 1 0.080 180.000 3.000 same as hc-c3-c
-o
O -C -OH-HO 1 2.300 180.000 -2.000 same as ho-oh-c
-o
O -C -OH-HO 1 1.900 0.000 1.000 same as ho-oh-c
-o
IMPROPER
CT-N -C -O 1.1 180.0 2.0 Using default
value
C -CT-N -H 1.1 180.0 2.0 Using default
value
CT-NB-CM-OS 1.1 180.0 2.0 Using default
value
CT-O -C -OS 1.1 180.0 2.0 Using default
value
CT-O -C -OH 1.1 180.0 2.0 Using default
value
NONBON
N3 1.8240 0.1700 same as n4
CT 1.9080 0.1094 same as c3
C 1.9080 0.0860 same as c
O 1.6612 0.2100 same as o
H 0.6000 0.0157 same as hn
HP 1.4870 0.0157 same as hc
HC 1.4870 0.0157 same as hc
N 1.8240 0.1700 same as n
H1 1.4870 0.0157 same as hc
CM 1.9080 0.0860 same as cc
OS 1.6837 0.1700 same as os
NB 1.8240 0.1700 same as nc
OH 1.7210 0.2104 same as oh
HO 0.0000 0.0000 same as ho
After that, when I run heating step, same problem occurs. When I use
generalized model, proton attached to side chain aspartic acids's oxygen is
not as agressive as in vacuum and cause no problem. However I have to
reproduce the MD simulation in vacuum. Decrasing the step size, heating
more gently, using different termostats, starting from different shape did
not work. Since I'm a biologist, developing a force field is far beyond my
skills, i think. What should I do? Thank you very much.
>
> Note that this tautomer was not considered in the Amber ff development:
> you'll
> have to develop of force field that is convincing in terms of its
> properties.
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
2013/5/3 David A Case <case.biomaps.rutgers.edu>
> On Fri, May 03, 2013, seçkin Boz wrote:
>
> > You likely have zero Lennard-Jones parameters on the proton bound to
> > oxygen.
> >
> > How can I add Lennard-Jones parameter for the proton?
>
> You'll need to define a new atom type for hydrogen bound to the side chain
> oxygen, and give it LJ parameters in the parm.dat (or frcmod) file.
>
> Note that this tautomer was not considered in the Amber ff development:
> you'll
> have to develop of force field that is convincing in terms of its
> properties.
>
> ...good luck...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue May 07 2013 - 02:00:02 PDT
