AMBER Archive (2008)

Subject: Re: AMBER: Torsional Forcing to generate PES?

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Tue Jan 08 2008 - 11:08:12 CST

raveena Gopal wrote:
> Dear Amber Users,
>
> I am using version 8 of AMBER for simulations. Is it possible to
> perfom torsion forcing to generate the complete potential energy
> surface for a simple peptide in AMBER.
>
> If so kindly suggest me an idea of doing it..
>
> Thanks in advance,
>
> PraveenaG
>

Here is a script that might give some inspiration. This script creates
input files to successively get energies every 15 degrees for a single
torsion in our "compounds 23" ligand. It uses a huge 500kCal penalty
barrier.

We have used this approach to quickly compare Amber energetics of our
developed parameters with QM torsion scan calculations in g03.

I suspect this script could be extended for multiple torsions. You'll
have to be extremely careful in your iat= atom selections for each
torsion. And, you have to subtract out restraint energies.
Perhaps most importantly, this is certainly NOT a "complete" PES - as we
are minimizing to a _local_ minimum from the start coordinates at each
15 degrees. And, scanning the torsion in fixed increments must be
inherently incomplete. (If you can find a way to give a "complete" PES
for any system, you will get a Nobel Prize- so best of luck :) )

#!/bin/tcsh -f
@ dihedral = 0

while ($dihedral < 360)
cat > cmpd23_dihedral.rst << eof
# RESTARINT FOR dihedral
# duplicates atom selection in QM calculation
 &rst
  iat=8,15,17,18, nstep1= 0, nstep2= 0,
  iresid= 0, ifvari= 0, ninc= 0, imult= 0, ir6= 0,
  r1= -1000.0, r2= $dihedral, r3= $dihedral, r4= 1000.0,
  rk2=500.0, rk3=500.0
 &end
eof
mkdir min$dihedral
echo min$dihedral
sander -O \
-i min.in -o min$dihedral/min_cmpd23.out -inf cmpd23.mininfo \
-p cmpd23.prmtop -c cmpd23.prmcrd \
-r min$dihedral/cmpd23_minimized.rst \
< /dev/null
ambpdb -p cmpd23.prmtop < min$dihedral/cmpd23_minimized.rst >
min$dihedral/cmpd23_minimized.pdb
@ dihedral += 15
echo $dihedral
end

P
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu