AMBER Archive (1999)

Subject: Re: distance restraint and ibelly

From: David Pearlman (David_Pearlman_at_vpharm.com)
Date: Wed Nov 17 1999 - 13:33:24 CST

on 11/17/99 8:35 AM, Nancy Bourassa wrote:
>
> > I am doing an energy minimization on RNA. During the minimization I want
> > to use distance and angle restraints and also belly atoms, but when I have
> > these two different restraints together, I receive an error message.
>

As always, you can void the trickiness of order dependence when doing
several special things with MD or Gibbs by using the Interface front end.

The Interface script below gives an example that includes a belly,
changing the temperature and imposing a distance restraint. Modifying
this for your own purposes should be trivial.

If you insist on NOT using the Interface front end, then simply run
the example below through Interface, to generate the intermediate input
file (md1.inp) and look at that file to see what goes where.

dap
------------------------------------------------------------------------
! Interface script that generates input to perform MD + belly + restraints

     sander
     md

     title = "generic title"
     time_limit = 9999999.0

     steps = 10000/runs=10
     read/formatted
     dielectric = 1
     pairlist / update = 25 / cutoff = 8.0
     pbc/volume/all_solute_nb
     report/steps = 50

     timestep = 0.0010

! set up the belly. Allow residues 1-110 to move

     belly
     group /residues=(1,110) /title = "residues 1-110 move"

! Use shake; Use standard temp. coupling with a single scale factor

     shake/toler=0.0005
     temp/target=300./constant=temp/tau_solute=0.20/initial= 10.0 \
         /coupling=single

! ramp up the temperature in the early stages, then hold at 300K

     change TEMP0 /from= 10.0/to= 300.0 /step1= 0/step2= 5000/every=5
     change TEMP0 /from= 300.0/to= 300.0 /step1= 5001/step2= 0

! Set up the distance restraint between atoms C1 in residues 1 and 2:
! Keep the distance fixed at 7.0A with a force constant of 100 kcal/mole.

    restraint /at1=1:C1 /at2=2:C1 \
              /step1 = 0 /step2 = 0 \
              /r1=5.0 /r2=7.0 /r3=7.0 /r4=9.0 \
              /k2=100.0 /k3=100.0

! read restraints from file restraints.list

     nmr /disang = "restraints.list" /listout = "restraints.final"

     generate /namelist /output=md1.inp

-------------------------------------------------------------------------- 

-- 
    David A. Pearlman                           email: dap_at_vpharm.com
Vertex Pharmaceuticals Inc.                    
130 Waverly St.                   "There are only 25 great people in the world &
Cambridge, MA 02139-4242         5 of them are hamburgers..." -- Cptn Beefheart