[AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch

From: tarak karmakar <tarak20489.gmail.com>
Date: Wed, 13 Jan 2016 19:12:37 +0530

Dear All,
I have a confusion related to two dihedral parameters that are present in
ffbonded.itp file,
 X OH P X 9 0.0 1.04600 3 ; JCC,7,(1986),230
 X OS P X 9 0.0 1.04600 3 ; JCC,7,(1986),230

the similar dihedral parameters from parm99SBgaff.dat (GAFF) file,
X -oh-p5-X 3 1.600 0.000 3.000
X -os-p5-X 3 2.400 0.000 2.000

As you see, there is a mismatch between the periodicity (last column) of
the similar dihedral angle from AMBER99SB and gaff databases.

Would anybody like to comment on this?
I just read an earlier discussion in the following link,
But, my problem is little more than the above.

I am currently simulating a protonated pyrophosphate ligand molecule in a
protein. During the heating step in NVT ensemble (within 150-200 ps, 200 K
temp), the atoms present in the phosphate groups (P,O and H) are showing
bizarre bonds and angles. I tried with the higher force constants (10 times
than the existing one) for the above mentioned dihedral angles, and then
the molecule was behaving fine.

Has anybody experienced this type of issue?
I appreciate any suggestions.

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Received on Wed Jan 13 2016 - 06:00:04 PST
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