Thank you for your reply and for your suggestion.
As I wrote, I made a mistake when I reported the commands that I used
in tleap, since I forgot the command "LoadAmberParams
frcmod.ionsjc_tip3p". Including this command, there are no errors.
I tried to use only Glycam06 parameters with tleap and sleap, but I
still have the same issues. Moreover, it seems that SHAKE does not
work, I try to restrain hydrogen bonds but I have no results.
However, I thank you again.
Tommaso Casalini, Ph.D. fellow,
CFA lab, Politecnico di Milano
Def. Quota "Karl N. Kirschner" <kkirsch.scai.fraunhofer.de>:
> Hi Tommaso,
>
> I have encountered a similar problem recently, I don't think it
> involves the glycam06g force field directly, but something with how
> xleap (didn't try tleap) interprets the force field when sourcing
> the protein/dna force field. If you look at the output structure of
> leap, I think you will see that a few of the hydrogen atoms are
> incorrectly placed. I corrected this by only loading glycam06
> parameters and suppressing the the protein force field loading (i.e.
> xleap -s -f leap.in). This then gave me the correct spatial
> structure of the carbohydrate. (I have not tried to reproduce this
> error using gleap or sleap.) However, if this works for you, then I
> think you will need to include the ions into glycam sourcing (I am
> pretty sure their parameters are sourced with the protein force
> field only, but not 100% sure about that).
>
> Cheers,
> Karl
>
> ----- Original Message -----
> From: "tommaso casalini" <tommaso.casalini.mail.polimi.it>
> To: amber.ambermd.org
> Sent: Friday, February 17, 2012 8:35:00 PM
> Subject: [AMBER] Issues with hydrogens using glycam force field in Amber 10
>
> 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 Sat Feb 18 2012 - 07:30:02 PST
