[AMBER] Modifying Parameters in parm7

From: Collin Nisler via AMBER <amber.ambermd.org>
Date: Fri, 30 Sep 2022 20:27:38 +0000

Hello Amber community, I am attempting to alter the parameters of a certain molecule in my system to match those generated by cgenff (in CHARMM format). Bonds and angles are fairly straightforward as far as I can tell, with the atom indices forming the bond/dihedral preceding the index for the given parameter. I'm a bit confused by the dihedrals, however, specifically for multi-term dihedrals. In CHARMM, a multi-term dihedral is just listed sequentially in the .prm file.

If I understand correctly, to add a multi-term dihedral in Amber, the 4 atoms forming the dihedral are listed in the DIHEDRALS_WITHOUT_HYDROGEN section as many times as there are terms in the dihedral with indices pointing to the associated force constant, multiplicity, and phase for each term, with all multiplicities for this dihedral being negative.

So, for example, if you have a dihedral with 3 terms, having multiplicity 1, 2, and 3, the 4 atoms forming this dihedral will be listed 3 times, each with a different index pointing to the specific parameters for each term (and each multiplicity being listed as -1, -2, and -3). Is this a correct interpretation? Does it matter in what order the dihedrals are listed in the DIHEDRALS_WITHOUT_HYDROGEN section as long as the index for the associated parameters is correct? Thanks very much.

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Received on Fri Sep 30 2022 - 14:00:03 PDT
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