AMBER Archive (2007)

Subject: Re: AMBER: torsional restraints in a solvated MD simulation.

From: Tom Pochapsky (pochapsk_at_brandeis.edu)
Date: Tue Aug 14 2007 - 18:11:27 CDT

Carlos Simmerling wrote:
> does sander tell you in the output file that it read the restraint input?
> it should have a section telling how many restraints it read, etc.
Carlos, Yes, it does read the constraint; the md.out file faithfully
describes it. However, no POUT is generated..
Thanks, TCP
>
> you might be better off changing the r1/r2/r3/r4 values using r1a/r2a/r3a/r4a
> rather than changing the REST weight. that way it will not have high forces and
> you can slowly shift it 180 deg.
>
> On 8/14/07, Tom Pochapsky <pochapsk_at_brandeis.edu> wrote:
>> 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
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