Thanks Ross,
I would be really like to know how to do this in amber 10, I'll send the
email.
All linkage parameters are available in GLYCAM_06
Lekpa.
On Wed, Mar 24, 2010 at 5:00 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Lekpa,
>
> > I need some advice regarding FF parameters.
> >
> > I have a molecule where a covalent bond exists between a peptiod and a
> > sugar. Parameters exist in AMBER and GLYCAM respectively for each but
> > due to
> > scaling (dihedral rotamer population is important in my work)issue with
> > SCEE and SCNB I have derived charges for the peptiod using the GLYCAM
> > approach ( ~200 structures from MD, CHelpG, 0.01 wt etc ). This is
> > relatively easy as my system is small. MD using the new charges (
> > without
> > SCEE/SCNB scaling of course and using AMBER valence parameters ) yield
> > very
> > similar structures (rsmd) in solution as model using parm99SB charges.
> >
> > I am thinking this is probably fine but I would like people's opinion!
>
> This seems reasonable 'except' that the parameters in AMBER, specifically
> the dihedral terms assume default SCEE=1.2 and SCNB=2.0. Thus you would
> have
> to re-parameterize the dihedrals as well. You should note that AMBER 11 (to
> be released in a few weeks) will address this issue allowing variable 1-4
> scaling to be done. AMBER 10 supports this in PMEMD (NOT sander) after
> applying bugfix.26. Thus you may want to wait until AMBER 11 or if you want
> to use AMBER 10 email me off list and I'll explain how to setup the
> relevant
> sections of the prmtop that you will need. This will let you use the
> standard charge and dihedral parameters for both GLYCAM and FF99SB
> together.
> You will still need to provide covalent parameters for the FF99SB to GLYCAM
> bond, angle and dihedrals.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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>
>
>
>
>
>
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Received on Wed Mar 24 2010 - 16:30:04 PDT
