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. 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
/
DISANG=RST2.dist
/
RST2.dist
#
# 74 SER OG 114 HID NE2 3.2
&rst
ixpk= 0, nxpk= 0, iat=1176,1838, r1= 1.30, r2= 1.80, r3= 3.20, r4= 3.70,
rk2=50.0, rk3=50.0, ir6=1, ialtd=0,
# 74 SER OG 9 LYS C 3.2
&rst
ixpk= 0, nxpk= 0, iat=1176,138, r1= 1.30, r2= 1.80, r3= 3.20, r4= 3.70,
rk2=50.0, rk3=50.0, ir6=1, ialtd=0,
&end
The command for minimization running was :
pmemd.cuda -O -i min2.in -o min2.out -p ../*.prmtop -c ../1_/*.rst -r
mc_min2.rst -ref ../1_/*.rst &
*****************************
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 Sun, Jul 5, 2015 at 4:06 PM, David A Case <david.case.rutgers.edu> wrote:
> On Sun, Jul 05, 2015, Michael Shokhen wrote:
> >
> > Thank you for the specifying the manual pages in chapter 24.1.
> > Unfortunately the mentioned text is very brief and insufficient for a
> > new user as me.
>
> > I would appreciate if you could give a detailed example of input file
> > for minimization and MD simulation accounting interatomic distance
> > restraints for one or two atomic pairs.
>
> Please consult section 24.11 ("Some sample input files"), and especially
> Section 24.11.2, which seems to provide what you are asking for.
>
> ...dac
>
>
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Received on Mon Jul 06 2015 - 09:00:02 PDT
