Re: [AMBER] ideal range values for distance restraint b/w 2 non-bonded atoms.

From: GG Smith <>
Date: Sat, 7 Mar 2015 19:26:18 +0530

Dear Dr.Jason,

Thanks a bunch for your quick response. Am using AMBER12 (ff12SB) .

*Am trying to position a nucleic acid duplex with enzyme by imposing
(Guiding) a specific distance between them (between side chain of certain
amino acid and phosphate backbone atom.

*The starting distance between them was ~ 7 Angstrom and i want it in range
of ~4.8 A.

# 16 ASN ND2 42 DNA O1P
 ixpk= 0, nxpk= 0, iat= 292, 1317, r1= 4.30, r2= 4.80, r3= 4.90, r4= 5.40,

*So during equilibration process of free energy minimization, i imposed
this condition. I was able to achieve it to near value by setting rk2 & rk3
to 20 kcal/mol. I continued it in pre-equil production run and then for ~
5ns production run. But during last 1 ns i see the Watson & crick paired
bases not maintaining planarity & at times losing hydrogen bond and duplex
structure distorted a bit. I have a doubt that whether this is due to
continued restraint during production run MD too.

My aim was to release the restraint and then do free simulation if still
tries to maintain same geometry and study other conformational features

(Prof.David case & Prof. Cheatham, would be grateful if can please. provide
your views/suggestions too on above situation)

I have done MD simulation for the same system without restraint and the
duplex looks fine, at least the hydrogen bonds between WC paired bases are

My concern is also whether this force constant value is leading to higher
frequency of vibration and is it affecting my overall results.Secondly, Is
this the right way to do or am I pushing my results to be biased? (Prof.

Deeply appreciate your time, valuable suggestions and help.


On 7 March 2015 at 18:00, Jason Swails <> wrote:

> > On Mar 7, 2015, at 6:22 AM, GG Smith <> wrote:
> >
> > Dear Amber Users,
> >
> > Am trying a simulate a protein+nucleic acid complex. I would like to
> > restrain distance between atoms of interest at particular distance
> > geometry for few ns in production run itself (sought of guided
> > simulation) and then do a free simulation. But am not sure of the
> > force constant to use for restraining the atoms mentioned in list
> > rst.dist (in my case). Pls. find below my input files.
> >
> > I would like to know What is ideal range for 1) restraint_wt and 2)
> > rk2 and rk3. Request to offer your insights and see if am going right.
> Note that your “restraint_wt” is not doing anything in your simulation.
> It corresponds only to the positional restraints set with ntr=1. I usually
> use force constants between 1 and 10 for positional restraints. For the
> flat-well NMR restraints, the strengths of the force constants you should
> use depend on what you are trying to accomplish with them. Since you have
> a distance range that is unbiased, a larger force constant seems warranted
> for violations. So I would say it looks fine (but it’s obviously more
> important how it affects your simulation than what I think).
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sat Mar 07 2015 - 06:00:02 PST
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