[AMBER] parameters from frcmod not overwriting gaff.dat

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From: Allen, Scott Edward <allense.email.unc.edu>
Date: Tue, 7 Jan 2014 17:11:24 +0000

Hello,

I am using tleap with the following script:

source leaprc.gaff
MOL = loadmol2 SEA_unc_78c_GAparam.mol2
LoadAmberParams SEA_unc_78c_GAparam.frcmod
SaveAmberParm MOL SEA_unc_78c_GAparam.prmtop SEA_unc_78c_GAparam.inpcrd
quit

My frcmod has explicit parameters for the X-cd-c -X dihedral (as in, I explicitly define all 4 dihedrals about this bond), but when I run rdparm --> printDihedrals on the resulting prmtop file, I see my parameters AND the parameters from gaff.dat defining all the X-cd-c -X dihedrals. I can work around this by deleting all gaff.dat-originating dihedrals manually in rdparm, or by using my own gaff.dat with the X-cd-c -X dihedrals deleted, but aren't the dihedrals from frcmod supposed to overwrite the ones from gaff.dat?

Thanks,
Scott

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Received on Tue Jan 07 2014 - 09:30:02 PST