Re: [AMBER] How to set interatomic distance restraint?

From: Michael Shokhen <>
Date: Mon, 6 Jul 2015 18:43:08 +0300

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 script.

I would appreciate your comments on the the presented below

scripts and RST2.dist.

 Thank you,


 minimization whole system

restraint distances: Ser74:OG-His114:NE2; Ser74:OG-Lys9:C


imin = 1,

maxcyc = 4000,

ncyc = 2000,

ntb = 1, iwrap = 1,

ntr = 0,

cut = 10.0






# 74 SER OG 114 HID NE2 3.2


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


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,


 The command for minimization running was :

 pmemd.cuda -O -i -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

On Sun, Jul 5, 2015 at 4:06 PM, David A Case <> 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
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