Dear Amber developers and users,
I have a problem with hydrogens, using GLYCAM_06 force field with Amber 10.
Glycam parameters version is Glycam_06g.dat.
I built hyaluronic acid dodecamer thanks to tleap, since I have to
investigate BMP2/HA interactions.
However, performing MD simulations and studying trajectories, I found
these problems:
1) C-H bond stretches a lot even if I apply SHAKE;
2) hydrogen atoms of methyl and hydroxyl groups rotate, it seems that
dihedral force constant is null or something like that.
There are some details:
I built hyaluronic acid with tleap, loading GLYCAM_06 parameters.
The HA chain is a sequence of 3YB and 4ZP units, saturated with OME groups.
I did not load any .frcmod file in order to modify ff parameters.
I performed simulations both in implicit and explicit solvent, but I
can see these issues in both cases.
It is very important for me that hydrogens are described properly,
since hydrogen bonding is an important interaction in the system I am
investigating.
I thank in advance for your help!
Tommaso Casalini, Ph.D Fellow
CFA lab, Politecnico di Milano
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Received on Fri Feb 17 2012 - 04:00:01 PST
