AMBER Archive (2004)

Subject: Re: AMBER: torsion scan

From: Furse, Kristina Elisabet (kristina.e.furse_at_vanderbilt.edu)
Date: Tue Jul 13 2004 - 12:37:35 CDT

Don't know about your iat section--I typically use:
iat=1,2,5,8,
with all 4 atom numbers sequentially instead of listing individually, but I use
amber7, not 8 (yet), so your way might work, too. The force looks a little high,
so maybe that's why you're not seeing a whole lot of resistance. Have you looked
at the trajectory (vmd or mddisplay) to see if the torsion is really moving?
I've rotated dihedrals before in order to do umbrella sampling, but I typically
break out the restraints in the DISANG file as follows:

#
# Drive to 75deg
 &rst
  iat=1,2,5,8, nstep1= 500001, nstep2= 600000,
  iresid= 0, ifvari= 1, ninc= 0, imult= 0, ir6= 0,
  r1= 30.0, r2= 60.0, r3= 60.0, r4= 90.0,
  rk2=1.0, rk3=1.0,
  r1a= 45.0, r2a= 75.0, r3a= 75.0, r4a= 105.0,
  rk2a=5.0, rk3a=5.0,
 &end
#
# Equilbration at 75deg
 &rst
  iat=1,2,5,8, nstep1= 600001, nstep2= 700000,
  iresid= 0, ifvari= 0, ninc= 0, imult= 0, ir6= 0,
  r1= 45.0, r2= 75.0, r3= 75.0, r4= 105.0,
  rk2=5.0, rk3=5.0,
  r1a= 45.0, r2a= 75.0, r3a= 75.0, r4a= 105.0,
  rk2a=5.0, rk3a=5.0,
 &end
#
# Data collection at 75deg
 &rst
  iat=1,2,5,8, nstep1= 700000, nstep2= 1000000,
  iresid= 0, ifvari= 0, ninc= 0, imult= 0, ir6= 0,
  r1= 45.0, r2= 75.0, r3= 75.0, r4= 105.0,
  rk2=5.0, rk3=5.0,
  r1a= 45.0, r2a= 75.0, r3a= 75.0, r4a= 105.0,
  rk2a=5.0, rk3a=5.0,
 &end
#
# Drive to 90deg
etc.

Good luck!
Kristina

Quoting Guanglei Cui <cuigl_at_csb.sunysb.edu>:

> Dear all,
>
> I'm trying to rotate along a dihedral angle by 360 degrees with nmropt =
> 1 in amber8. Here is the DISANG file
>
> &rst
> iat(1) = 11565, iat(2) = 11567, iat(3) = 11568, iat(4) = 11569,
> nstep1 = 1, nstep2 = 360000, irstyp = 0, ifvari = 1,
> r1 = 165.021, r2 = 170.021, r3 = 170.021, r4 = 175.021,
> r1a = 525.021, r2a = 530.021, r3a = 530.021, r4a = 535.021,
> rk2 = 5000, rk3 = 5000, rk2a = 5000, rk3a = 5000,
> &end
> &rst
> iat(1) = 0,
> &end
>
> From the output, I can see this restraint is read and applied. But from
> the value of restraint energy (fairly small), it doesn't seem to me the
> r2 and r3 are being varied during the calculation. Is there a mistake in
> the input or did I misunderstand the manual? Any input is very appreciated.
>
> Guanglei
>

-----------------------------------------------------------------
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
Email: kristina.e.furse_at_Vanderbilt.Edu
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