Dear Jason,
Many thanks for your expertise.
The problem is resolved now.
All the best,
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: michael.shokhen.gmail.com
email: shokhen.mail.biu.ac.il
On Mon, Jul 6, 2015 at 7:00 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Jul 6, 2015 at 11:43 AM, Michael Shokhen <
> michael.shokhen.biu.ac.il>
> wrote:
>
> > Dear David,
> >
> >
> > Sorry bother you again but I guess that
> >
> > I failed to correctly generate script for
> >
> > minimization with restraint despite I carefully studied
> >
> > the recommended chapter 24 in the amber 15 manual.
> >
> >
> > My task is to relax by productive MD simulation a
> >
> > Michaelis complex (MC) of enzyme with peptide substrate.
> >
> > Enzyme is a serine protease, so the interatomic distance (d1) between
> >
> > carbonyl carbon atom of substrate and nucleophilic oxygen atom
> >
> > of catalytic Ser should be around 3 A. Approximately the same
> > distance 3 A (D2) must be between N eps atom of general base catalytic
> > His and Ser oxygen. These interatomic distances are the key parameters
> >
> > for correct MC structure. I assumed that the conditional structure
> > relaxation of MC by MD simulation can be controlled by the
> >
> > restraint minimization algorithm implemented in amber
> > using the predefined d1 and d2 restraint interatomic distances.
> >
> >
> > Based on previously constructed by molecular modeling MC the initial
> >
> > distance values were d1 = 3.9 A and d2 = 2.8 A.
> >
> >
> > Unfortunately, even at the stage of preliminary minimization
> >
> > the d1 = 4.6 A demonstrated irrelevant value.
>
>
> I'm not sure what you mean by "irrelevant value"...
>
>
>
> > The other distance
> > d2 =2.9 A is reasonable. I should to stress that the same result was
> >
> > when I used non-restraint minimization. Thus I suggested that
> >
> > I incorrectly constructed the restraint file and also incorrectly
> >
> > call it form min2.in script.
> >
> > I would appreciate your comments on the the presented below
> >
> > scripts min2.in and RST2.dist.
> >
> >
> > Thank you,
> >
> > Michael
> >
> >
> > min2.in
> >
> >
> > minimization whole system
> >
> > restraint distances: Ser74:OG-His114:NE2; Ser74:OG-Lys9:C
> >
> > &cntrl
> >
> > imin = 1,
> >
> > maxcyc = 4000,
> >
> > ncyc = 2000,
> >
> > ntb = 1, iwrap = 1,
> >
> > ntr = 0,
> >
> > cut = 10.0
> >
>
> You never turned the distance restraints on. You need to set nmropt=1 to
> do that.
>
> See some examples in $AMBERHOME/test/nmropt/pme/distance (the input files
> are generated in Run.dist_pbc).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 09 2015 - 01:30:02 PDT
