Dear All
I have a question about the parameter file for example for BMI ion (organic
cation in ionic liquids). In the parmchk step we calculate the new
parameters and save in the frcmod.bmi (for example) file. If the *-a y *option
is added to parmchk all of the parameters (all of them) is printed to the
file. If I change some of the old parameters in the frcmod.bmi file and run
MD simulation the old parameters are used or the modified parameters in the
frcmod.bmi file?
Your Sincerely
S. Nasiri
===============================================================
* parmchk -i bmi.mol2 -f mol2 -o frcmod.bmi*
*frcmod.bmi*
remark goes here
MASS
BOND
ANGLE
na-cc-na 73.650 109.330 same as na-c2-na
DIHE
IMPROPER
h5-na-cc-na 1.1 180.0 2.0 Using default
value
c3-cc-na-cc 1.1 180.0 2.0 Using default
value
c3-cc-na-cd 1.1 180.0 2.0 Using default
value
cd-h4-cc-na 1.1 180.0 2.0 Using default
value
cc-h4-cd-na 1.1 180.0 2.0 Using default
value
NONBON
=============================================================
* parmchk -a y -i bmi.mol2 -f mol2 -o frcmod.bmi*
*frcmod.bmi*
remark goes here
MASS
cc 12.010 0.360
na 14.010 0.530
cd 12.010 0.360
c3 12.010 0.878
h5 1.008 0.135
hc 1.008 0.135
h1 1.008 0.135
h4 1.008 0.135
BOND
cc-na 438.80 1.371
cc-h5 356.00 1.079
na-c3 334.70 1.456
na-cd 438.80 1.371
cc-cd 504.00 1.371
cc-h4 350.10 1.083
cd-h4 350.10 1.083
c3-h1 335.90 1.093
c3-c3 303.10 1.535
c3-hc 337.30 1.092
ANGLE
cc-na-cc 68.940 109.900
cc-na-c3 62.560 125.090
cc-na-cd 63.880 128.010
na-cc-na 73.650 109.330 same as na-c2-na
na-cc-h5 49.760 122.100
na-cc-cd 72.910 109.420
na-cc-h4 50.220 119.660
na-c3-h1 49.900 109.450
na-cd-cc 72.910 109.420
na-cd-h4 50.220 119.660
na-c3-c3 65.730 112.810
cc-cd-h4 47.190 129.110
cd-na-c3 62.560 125.090
cd-cc-h4 47.190 129.110
c3-c3-c3 63.210 110.630
c3-c3-hc 46.370 110.050
c3-c3-h1 46.360 110.070
hc-c3-hc 39.430 108.350
h1-c3-h1 39.180 109.550
DIHE
cc-na-cc-cd 1 1.700 180.000 2.000
cc-na-cc-h4 1 1.700 180.000 2.000
cc-na-c3-h1 1 0.000 0.000 2.000
cc-na-cd-cc 1 1.700 180.000 2.000
cc-na-cd-h4 1 1.700 180.000 2.000
cc-na-c3-c3 1 0.000 0.000 2.000
na-cc-na-cd 1 1.700 180.000 2.000
na-cc-na-c3 1 1.700 180.000 2.000
na-cc-cd-na 1 4.000 180.000 2.000
na-cc-cd-h4 1 4.000 180.000 2.000
na-cc-na-cc 1 1.700 180.000 2.000
na-cd-cc-h4 1 4.000 180.000 2.000
na-c3-c3-c3 1 0.156 0.000 3.000
na-c3-c3-hc 1 0.156 0.000 3.000
cc-na-cc-h5 1 1.700 180.000 2.000
cc-cd-na-c3 1 1.700 180.000 2.000
cd-na-cc-h5 1 1.700 180.000 2.000
cd-na-c3-c3 1 0.000 0.000 2.000
cd-na-c3-h1 1 0.000 0.000 2.000
cd-cc-na-c3 1 1.700 180.000 2.000
c3-na-cc-h5 1 1.700 180.000 2.000
c3-na-cc-h4 1 1.700 180.000 2.000
c3-na-cd-h4 1 1.700 180.000 2.000
c3-c3-c3-c3 1 0.180 0.000 -3.000
c3-c3-c3-c3 1 0.250 180.000 -2.000
c3-c3-c3-c3 1 0.200 180.000 1.000
c3-c3-c3-hc 1 0.160 0.000 3.000
c3-c3-c3-h1 1 0.156 0.000 3.000
hc-c3-c3-hc 1 0.150 0.000 3.000
h4-cc-cd-h4 1 4.000 180.000 2.000
h1-c3-c3-hc 1 0.156 0.000 3.000
IMPROPER
h5-na-cc-na 1.1 180.0 2.0 Using default
value
c3-cc-na-cc 1.1 180.0 2.0 Using default
value
c3-cc-na-cd 1.1 180.0 2.0 Using default
value
cd-h4-cc-na 1.1 180.0 2.0 Using default
value
cc-h4-cd-na 1.1 180.0 2.0 Using default
value
NONBON
cc 1.9080 0.0860
na 1.8240 0.1700
cd 1.9080 0.0860
c3 1.9080 0.1094
h5 1.3590 0.0150
hc 1.4870 0.0157
h1 1.3870 0.0157
h4 1.4090 0.0150
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Received on Wed Dec 25 2013 - 08:30:02 PST
