[AMBER] Reg: Query on distance restrain and its effect on conformation

From: GG Smith <ggsmithibab.gmail.com>
Date: Wed, 11 Mar 2015 00:41:18 -0400

Dear Amber Users,

Am a graduate student venturing recently in to dynamics, I
would like to humbly seek your advice and suggestion regarding a
simulation attempted by me on Protein+nucleic acid complex .

I had written to amber forum about the ideal range force constant to
be used for restraining distance b/w specific residues of protein &
nucleic acid backbone. I was suggested to use ~ 20 kcal/mol. Am using
AMBER12 (ff12SB) program.

Pls. find below the steps i followed:

*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 wanted it
in range of ~5.0 A.

This is my restraint file;

# 16 ASP OD2 42 DNA O1P
 ixpk= 0, nxpk= 0, iat= 292, 1317, r1= 4.30, r2= 4.80, r3= 4.90, r4= 5.40
    rk2=20.0, rk3=20.0, ir6=1, ialtd=0,

*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 of production run. But during last 1 ns i see that some
Watson & crick paired bases are 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.

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

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

**My concern is 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?

Appreciate your valuable suggestions and help and time.

Warm Regards
AMBER mailing list
Received on Tue Mar 10 2015 - 22:00:02 PDT
Custom Search