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
Received on Mon Jul 06 2015 - 09:30:02 PDT
