AMBER Archive (2004)

Subject: Re: AMBER: target rmsd

From: Viktor Hornak (hornak_at_csb.sunysb.edu)
Date: Mon Sep 13 2004 - 15:57:07 CDT


Also check the formatting of your input sections - see comments below in
the input you included...

Cheers,
-Viktor

Carlos Simmerling wrote:
> Bill,
>
> Bill,
> it doesn't look like you set nmropt=1 to read the weight changes.
> does the sander output actually list the changing target under "Begin
> reading energy term weight
> changes"? does that echo what you told it to do?
>
> take a look at the test case for changing target,
> amber8/test/tgtmd/change_target.ntr.
> that should be a good template for the correct format.
>
> even if you resolve that, it might be hard to get from 2.0A to 0.5
> directly without getting stuck.
> to verify that it's working you might try going the other way first,
> from 0.5 to 2A
> since that should be easier. also see if the restraint energy is going up
> as you reduce the target, since the force from the tgtmd might not be
> enough to
> overcome something that's keeping the system from reducing the rmsd
> (such as
> a side chain trapped somewhere, etc).
>
> cheers
> Carlos
>
> ===================================================================
> Carlos L. Simmerling, Ph.D. Associate Professor Phone: (631)
> 632-1336 Center for Structural Biology Fax: (631) 632-1555
> Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
> Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
> ===================================================================
>
>
> William Andrew McLaughlin wrote:
>
>> To anyone who may be helpful:
>>
>> I am trying to use targetted rmsd function for a molecular dynamics
>> simulation. I would like to vary the rmsd level of the protein backbone
>> during the simulation and have tried to use the weight function. My
>> molecular dynamics input file is shown below. As you can see I am trying
>> to vary the target rmsd from 2 anstroms (value1) down to 0.5 angstroms
>> (value2). When I run the simulation it appears that the rmsd value does
>> not vary and just stays at the second value of 0.5 angstrom rmsd. Any
>> ideas on how to vary the target rmsd for the backbone during the
>> simulation would be helpful.
>>
>> Sincerely,
>>
>> Bill McLaughlin
>>
>> short molecular dynamics simulation
>> &cntrl
>> imin = 0, ntb = 0,
>> igb = 0, ntpr = 100, ntwx = 100,
>> ntt = 3, gamma_ln = 1.0,
>> tempi = 300.0, temp0 = 300.0
>> nstlim = 100000, dt = 0.001, nscm=1,
>> cut = 999,
>> ntr=1,
>> restraint_wt=1.0,
>> restraintmask=':2',
>> ITGTMD=1,
>> tgtrmsmask='@CA,C,O,N,H',
>> tgtmdfrc=1,
>> tgtrmsd=0.6,
" /" missing here?

>> &wt type='TGTRMSD',istep1=0,istep2=100000,value1=2.0, value2=0.5,
and here " /"

>> &wt type='END',
>> &end,
use " /" rather than &end (comma after &end?)
>> /
...??? - this slash is probably mistyped too...
>>
>> William McLaughlin, Ph.D.
>> Dept. of Chemistry and Biochemistry
>> 9500 Gilman Drive
>> 4th Floor Urey Hall
>> La Jolla, California 92093-0359
>>
>> Email: wimclaug_at_popmail.ucsd.edu
>> Phone: (858) 822-4240
>> Fax: (858) 534-7042
>>

-- 
===================================================================
Viktor Hornak
Center for Structural Biology   Phone: (631)632-1439
SUNY at Stony Brook             Fax:   (631)632-1555
Stony Brook, NY 11794-5115      E-mail: viktor.hornak_at_sunysb.edu
===================================================================
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