Hi,
I have a molecule that i would like to use in my simulation, i can get
the missing parameters from Antechamber, but i prefer to get the charges
from antechamber but use the forcefield already defined in gaff.dat.
However, in xleap i get missing parameters
Checking parameters for unit 'smcc'.
Checking for bond parameters.
Checking for angle parameters.
Could not find angle parameter: c3 - n3 - c2
Could not find angle parameter: c3 - n3 - c2
Could not find angle parameter: n3 - c2 - c3
Could not find angle parameter: n3 - c2 - o
Could not find angle parameter: n3 - c2 - c3
Could not find angle parameter: n3 - c2 - o
There are missing parameters.
check: Warnings: 4
Unit is OK.
i looked at the 'Development and Testing of a General Amber Force Field'
article and i am still not sure why would gaff not have the above
parameters unless there is something wrong with my atom types or my
structure. What is the atom type of a nitrogen connected to three
carbons? as far as i can tell it should be n3.
also, since i sent the mol2 file, the bond between c2 and o is a double
bond, shouldn't there be a number 2 in the fourth column under
.<TRIPOS>BOND? unless the number in the fourth column is inconsequential
since the bond force and length in the forcefield file is what matters.
Thank you for your help,
Taufik
Received on Fri Jun 05 2009 - 01:13:13 PDT
