Hello Amber users.
I have a general question regarding generating topology file using
antechamber.
Let's say I have a mol2 file. I load the mol2 file in leap and generate
topology file after checking the unit using the command
check SUS
The result is
Checking 'sus'....
Checking parameters for unit 'sus'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
Now I have not loaded the frcmod file for this molecule since the leap said
the unit is ok and there were no missing parameters.
However I load the frcmod file (as given below)
remark goes here
MASS
BOND
ANGLE
DIHE
IMPROPER
ca-ca-ca-ha 1.1 180.0 2.0 General
improper torsional angle (2 general atom types)
ca-ca-ca-os 1.1 180.0 2.0 Using default
value
c3-n -c -o 10.5 180.0 2.0 General
improper torsional angle (2 general atom types)
NONBON
And now I generate the topology file.
The topology generated before and after using the frcmod file is not the
same i.e the number of dihedrals is not the same.
Should I be concerned ?
Which topology is correct
Arun
Thanks
Arun
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Received on Wed Jun 24 2015 - 10:30:02 PDT
