AMBER Archive (2008)

Subject: Re: AMBER: Need help... High energies for complex...

From: Neha Gandhi (n.gandhiau_at_gmail.com)
Date: Wed Sep 03 2008 - 07:41:16 CDT

Hi,

Are you using charged carbohydrate such as heparin? Is there any drastic
conformational change in receptor-carbohydrate complex? Are you using the
coordinates from last snapshot to calculate the energies or you are starting
with the initial complex?

Regards,
Neha

2008/9/3 Carlos Simmerling <carlos.simmerling_at_gmail.com>

> what do you get for energies if you simply separate the complex and do
> sing point energy? you need to see if it's a problem in your protocol
> for the minimization or if there is something that doesn't match in
> the prmtop files. perhaps it's not the same parameters or force field
> for the individual units as they have in the complex. I would suggest
> using exactly the same procedure, restraints and all, on all parts of
> your calculation (complex and separated).
>
> On Wed, Sep 3, 2008 at 7:45 AM, Waqas Nasir <nasirwaqas1983_at_yahoo.com>
> wrote:
> > Yes, it was the same for single point energy calculations and the
> complex. I
> > did it for snapshots both with and without restraints. But results dont
> seem
> > to differ much...
> > The main minimization on complex was with restraints on one of the sugar
> > rings.
> >
> > ----- Original Message ----
> > From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> > To: amber_at_scripps.edu
> > Sent: Wednesday, September 3, 2008 2:27:06 PM
> > Subject: Re: AMBER: Need help... High energies for complex...
> >
> > did you use the same minimization procedure on the complex?
> >
> > On Wed, Sep 3, 2008 at 7:20 AM, Waqas Nasir <nasirwaqas1983_at_yahoo.com>
> > wrote:
> >> Hi,
> >>
> >> Hope every one is doing fine.
> >>
> >> Well, I have done some manual single point energy calculations on my
> >> protein
> >> carbohydrate complex using amber version 8. The protein is a dimmer and
> >> the
> >> sugar is a tetra-saccharide. The values for the binding energy that I am
> >> getting are quite high and are in the order of negative 3500-4500 kcal.
> >>
> >> The script that I have used breaks each of 250 frames in my md run into
> >> separate protein and sugar subunits. Minimization of about 500 steps is
> >> then
> >> performed on each subunit followed by single point md (one with 0 time
> >> steps). The energies from sugar and protein md runs for a single frame
> are
> >> added up. The difference of this value is then taken with the actual
> >> energy
> >> of the complex, that results is ridiculously high values.
> >>
> >> Just wanted to have some thoughts on what might have gone wrong in these
> >> calculations. Or, what steps one might take to improve the results in
> >> general.
> >>
> >> Any sort of check list is highly appreciated.
> >>
> >> Thanks a lot for reading...
> >> Stay blessed!
> >>
> >> Regards,
> >> Waqas.
> >>
> >>
> >>
> >
> >
> >
> > --
> > ===================================================================
> > Carlos L. Simmerling, Ph.D.
> > Associate Professor Phone: (631) 632-1336
> > Center for Structural Biology Fax: (631) 632-1555
> > CMM Bldg, Room G80
> > Stony Brook University E-mail: carlos.simmerling_at_gmail.com
> > Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> > ===================================================================
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
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> >
> >
>
>
>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> CMM Bldg, Room G80
> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> ===================================================================
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
> 

-- 
Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845

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