AMBER Archive (2006)

Subject: Re: AMBER: Values of Spring Constants

From: Sai Kumar Ramadugu (compchem123_at_gmail.com)
Date: Wed Feb 01 2006 - 09:43:05 CST

Dear Sir,
   Actually I was trying to understand the functioning of Umbrella Smapling.
For the same I took a protein of 40 aminoacids and did a GB simulation with
restraints on phi angle of 2nd amino acid which is Alanine.
    My restraints input file is as follows:
# 2 ALA PHI: (1 ASP C)-(2 ALA N)-(2 ALA CA)-(2 ALA C) 120.0 180.0
 &rst iat = 13, 15, 17, 23,
          r1 = 119.0, r2 = 120.0, r3 = 180.0, r4 = 181.0,
          rk2 = 2.0, rk3 = 2.0, &end

 My sander input file is as follows:

test of umbrella sampling of a phi torsion angle
 &cntrl
   nstlim=100000, cut=99.0, igb=1, saltcon=0.1,
   ntpr=10, ntwr=1000000, ntwx=1000, ntt=3, gamma_ln=0.0,
   ntx=5, irest=1,
   ntc=2, ntf=2, tol=0.000001,
   dt=0.001, ntb=0,
   nmropt=1,
 /
 &wt type='DUMPFREQ', istep1=10 /
 &wt type='END' /
DISANG=restraints1.RST
DUMPAVE=phi_120
LISTIN=POUT
LISTOUT=POUT

Thanks and regards,
   Sai

On 2/1/06, Carlos Simmerling <carlos_at_ilion.bio.sunysb.edu> wrote:
>
> this is not supposed to be the values from the parm99.dat
> file, it is the value of the harmonic force that YOU added
> for the umbrella potential. it's hard to say more since you
> didn't give any detail, or your sander input, etc.
>
> Sai Kumar Ramadugu wrote:
> > Dear All,
> > I wanted to do a simulation using the Umbrella Sampling. For
> > restraints I was using the Phi torsional angle of a residue. As it was
> > mentioned in AMBER manual to use WHAM to generated the potential of
> > mean force, I used WHAM. But in the WHAM program it asks for the
> > values of the spring (foce) constant for the restraining potential.
> > How can I get the value of the spring constant for the Phi angle
> > between N-C-CA-N. I looked at the parm99.dat file but there were four
> > columns for the torsinal angles. Now which one among them could be the
> > values of force constant? Please help me in this regard.
> > Thanks and regards,
> > Sai
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