AMBER Archive (2004)

Subject: Re: AMBER: target rmsd

From: William Andrew McLaughlin (wimclaug_at_popmail.ucsd.edu)
Date: Mon Sep 13 2004 - 16:40:24 CDT

Dear Viktor and Carlos,

Thank you for the help: I set nmropt=1 and reformated as prescribed. The
rmsd during the simulation does then vary appropriately. FYI I changed
the tgtmdfrc from 1 to 5000 and there is no energy barriers that appeared
not to be overcome. Also, FYI I am using the function to do sampling of
possible backbone conformations with a structure solved through X-ray
crystallography. Since the function can be applied to non nmr structures
would it be more appropriate to not have it as and nmr option? Also, for
this purpose, would a program like MOIL be more appropriate?

Thank you much in advance.

Bill

> 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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>

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

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