This probably isn't the force field, but rather how you are setting up
or running your simulation.
Can you send me (or post) the commands you used in leap to build the
structures? Also, please include the mdin (control input) files.
On Fri, Feb 17, 2012 at 6:35 AM, <tommaso.casalini.mail.polimi.it> wrote:
> 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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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Fri Feb 17 2012 - 08:30:01 PST
