Hello
I am parametrizing an unnatural amino acid, phenylglycine (PHG), in
the OPLS FF in GROMACS. I have put in the necessary parameters in
the .hdb, .rtp, and the aminoacids.dat file.
1. When I do grompp for the EM, I get an error saying that I have not
put in the appropriate parameters for the bonds, angles and
dihedrals. Surprisingly, when I do put in the parameters (from the
ffoplsaabon.itp file), the angles, bonds, and dihedrals get even more
distorted, a counterintuitive observation. In fact the simulation is
much better off when I ignore the warnings and the program puts in
zeros after the required parameters in the .top file. Why is this
happening?
Another question related to this:
2. When I do parametrize a single peptide with a single PHG residue
and then simulate it (with zeros for the parameters in the .top
file), the PHG turns out fine and does not get distorted. But when I
simulate many PHG containing peptides, say 10 of them stacked on top
of and besides each other, I observe that some of the PHGs get
distorted while others don't. By distorted, I especially mean the
Halpha-Calpha-aromaticC angle, which gets distorted to almost 90 from
its normal value of about 109. Whatever the cause for this distortion
is, why is it affecting only some PHG residues and not others?
Thank you
Regards,
Ashutosh Jogalekar
Emory University.
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