I am trying to force a cis -> trans isomerization of a peptide bond
during a standard solvated MD simulation using Amber 8. I have
included a standard torsion restraint file to be applied gradually
during the simulation, but cannot detect any change; furthermore, no
torsional energies are reported in md.out , its as if the restraint is
not being applied. Any suggestions?
Thanks,
Tom Pochapsky
Here is the md control file and the restraint file.
md.in
> &cntrl
> imin=0, irest=1, ntx=7, tempi=0.0,
> ntt=3, temp0=300.0, tautp=1.0, nmropt=1,
> ntp=1, taup=2.0, nrespa=1,
> ntb=2, ntc=2, ntf=2,
> nstlim=60000, dt=0.001,
> ntwe=1000, ntwx=1000, ntpr=1000,
> gamma_ln=10,
> /
> #
> #weight change for cis ->trans isomerization
> #
>
> &wt type='REST',
> istep1=0,istep2=60000,value1=1.0,
> value2=10.0,
> /
>
>
>
> &wt type='END' /
> LISTOUT=POUT
>
> DISANG=RST
RST
> 84 PRO OMEGA: (83 CYS CA)-(83 CYS C)-(84 PRO N)-(84 PRO CA) -530.0 -180.0
> &rst iat = 1321, 1336, 1338, 1348,
> r1 = -531.0, r2 = -530.0, r3 = -180.0, r4 = -179.0,
> rk2 = 100.0, rk3 = 100.0, &end
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Aug 15 2007 - 06:07:56 PDT
