Hello,
I am attempting to fit several parameters using paramfit by generating modified geometries in tleap and feeding those coordinates into single-point QM calculations. My modified amino acid contains a partially-conjugated ring, so there are several improper torsions and a LOOP card in the prep file. Through trial-and-error, I have found that tleap's impose command does not work on bonds between LOOP atoms or dihedrals involving the central atom of an improper torsion. Is there a way to force impose to affect these atoms, or another simple way to do this?
I've recreated this issue below using the CRO residue prepin and frcmod files from tutorial B5 (
http://ambermd.org/tutorials/basic/tutorial5/). Here is the tleap input:
source leaprc.protein.ff14SB
loadAmberPrep cro.prepin
loadAmberParams frcmod2.cro
loadAmberParams frcmod1.cro
gfp = loadPDB gfp.pdb
impose gfp { 64 } { { "CA2" "N2" "C1" "CA3" 180.0 } }
impose gfp { 64 } { { "C2" "N3" 1.5 } }
saveAmberParm gfp gfp_impose.prmtop gfp_impose.mdcrd
quit
The resulting coordinate file is identical to using the same input without the impose lines, while using impose on other atoms in the CRO residue changes the resulting coordinates and gives the expected bond length, angle, or dihedral.
Thank you,
Kent Gorday
Oak Ridge National Laboratory
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Received on Wed Jun 28 2017 - 12:00:02 PDT
