Re: urestraint doesn't work

From: Michael Grabe (mgrabe_at_itsa.ucsf.edu)
Date: Thu Oct 27 2005 - 20:55:49 CDT

wei,

here is what i do. it is exactly what you have.
this works for me. barr=2000 is a little extreme
but i guess you are just testing it.
did the simulation run? do you get any errors
in the *.out file? does the *.out file echo
your restraints to you?

hmm. i am a little baffled by this. are you sure that
your segment is correct, and that your segment name
is in the correct position in the pdb line?

also, is your simulation shorter or longer than 1 ps?
make the simulation 1 step longer than the time of
the pmf or else it will stop doing the restraints.

-michael

freeEnergy on
freeEnergyConfig {
urestraint {

dist (CP2,308,CA) (S4,169,CA) kf=0.100 ref=12

dihe (S1 , 65,N ) (S1 , 65,CA) (S1 , 65,C ) (S1 , 66,N )
barr=200.00 ref=-113.698
}

pmf {
    task = stop
    time = 25 ps
  }
}

On Oct 27, 2005, at 7:45 PM, Wei Zhuang wrote:

> I tried the following:
>
> *********************
> freeEnergy on
> freeEnergyConfig {
>
> urestraint {
>
> dihe (TRZ4,1,C) (TRZ4,2,N) ( TRZ4,2,CA) (TRZ4,2,C) barr=2000.0
> ref=-155.40
>
> }
>
> pmf {
> task = stop
> time = 1 ps
> }
>
> }
>
> **********************
>
> and it doesn't work. any comment?
>
> Wei
>
>> yup.
>>
>> On Oct 27, 2005, at 6:35 PM, Wei Zhuang wrote:
>>
>>> Hi, Michael:
>>>
>>> Thanks for the prompt reply.
>>>
>>> But I used the Restraint Specifications, which is, indicated in the
>>> manual, "not coupled to pmf calculations". And there is no lambda in
>>> the expression, do I still need the pmf?
>>>
>>> Wei
>>>
>>>> hi wei,
>>>>
>>>> you need to use the PMF routine at the same time to make this work.
>>>>
>>>> -michael
>>>>
>>>> On Oct 27, 2005, at 2:56 PM, Wei Zhuang wrote:
>>>>
>>>>> Hi,all:
>>>>>
>>>>> I was trying to run a restrained-dihedralangle simulation, I put
>>>>> this
>>>>> paragraph in the .conf:
>>>>>
>>>>> *****************************
>>>>> freeEnergy on
>>>>> freeEnergyConfig {
>>>>>
>>>>> urestraint {
>>>>>
>>>>> dihe (TRZ4,1,C) (TRZ4,2,N) ( TRZ4,2,CA) (TRZ4,2,C) barr=2000.0
>>>>> ref=-155.40
>>>>>
>>>>> }
>>>>>
>>>>> }
>>>>>
>>>>> ********************************
>>>>>
>>>>> the script went through with no problem, but when I checked the
>>>>> output
>>>>> pdb file, it seems like there is no constraint at all, could
>>>>> anybody
>>>>> give me some help about what is going on here?
>>>>>
>>>>> Wei
>>>>>
>>>>>
>>>>>
>>>> --------------------------------------------------------------------
>>>> --
>>>> --
>>>> --------------------------
>>>> Michael Grabe, Ph.D.
>>>> Post-doctoral Fellow
>>>> Howard Hughes Medical Institute
>>>> University of California, San Francisco
>>>> 1550 4th Street GD482
>>>> San Francisco, CA 94143
>>>> mgrabe_at_itsa.ucsf.edu
>>>> tel: ++ 415.476.4021
>>>> http://itsa.ucsf.edu/~mgrabe
>>>>
>>>>
>>>> hi wei,
>>>>
>>>>
>>>> you need to use the PMF routine at the same time to make this work.
>>>>
>>>>
>>>> -michael
>>>>
>>>>
>>>> On Oct 27, 2005, at 2:56 PM, Wei Zhuang wrote:
>>>>
>>>>
>>>> <excerpt>Hi,all:
>>>>
>>>>
>>>> I was trying to run a restrained-dihedralangle simulation, I put
>>>> this
>>>> paragraph in the .conf:
>>>>
>>>>
>>>> *****************************
>>>>
>>>> freeEnergy on
>>>>
>>>> freeEnergyConfig {
>>>>
>>>>
>>>> urestraint {
>>>>
>>>>
>>>> dihe (TRZ4,1,C) (TRZ4,2,N) ( TRZ4,2,CA) (TRZ4,2,C) barr=2000.0
>>>> ref=-155.40
>>>>
>>>>
>>>> }
>>>>
>>>>
>>>> }
>>>>
>>>>
>>>> ********************************
>>>>
>>>>
>>>> the script went through with no problem, but when I checked the
>>>> output
>>>> pdb file, it seems like there is no constraint at all, could anybody
>>>> give me some help about what is going on here?
>>>>
>>>>
>>>> Wei
>>>>
>>>>
>>>>
>>>>
>>>> </excerpt><color><param>0202,6969,1212</
>>>> param>--------------------------------------------------------------
>>>> --
>>>> ----------------------------------</color>
>>>>
>>>> Michael Grabe, Ph.D.
>>>>
>>>> Post-doctoral Fellow
>>>>
>>>> <color><param>0202,6B6B,1212</param>Howard Hughes Medical Institute
>>>> </color>
>>>>
>>>> University of California, San Francisco
>>>>
>>>> 1550 4th Street GD482
>>>>
>>>> San Francisco, CA 94143
>>>>
>>>> mgrabe_at_itsa.ucsf.edu
>>>>
>>>> tel: ++ 415.476.4021
>>>>
>>>> <color><param>0000,0000,FFFF</param>http://itsa.ucsf.edu/~mgrabe
>>>> color>
>>>>
>>>>
>>>>
>>>
>>> = = = = = = = = = = = = = = = = = = = =
>>>
>>>
>>> $B!!!!!!!!!!!!!!!!CW(B
>>> $BNi!*(B
>>>
>>>
>>> $B!!!!!!!!!!!!!!!!(BWei Zhuang
>>> $B!!!!!!!!!!!!!!!!(
Bwzhuang_at_uci.edu
>>> $B!!!!!!!!!!!!!!!!!!!!(B2005-10-27
>>>
>>>
>>>
>>>
>> ----------------------------------------------------------------------
>> --
>> --------------------------
>> Michael Grabe, Ph.D.
>> Post-doctoral Fellow
>> Howard Hughes Medical Institute
>> University of California, San Francisco
>> 1550 4th Street GD482
>> San Francisco, CA 94143
>> mgrabe_at_itsa.ucsf.edu
>> tel: ++ 415.476.4021
>> http://itsa.ucsf.edu/~mgrabe
>>
>>
>> yup.
>>
>>
>> On Oct 27, 2005, at 6:35 PM, Wei Zhuang wrote:
>>
>>
>> <excerpt>Hi, Michael:
>>
>>
>> Thanks for the prompt reply.
>>
>>
>> But I used the Restraint Specifications, which is, indicated in the
>> manual, "not coupled to pmf calculations". And there is no lambda in
>> the expression, do I still need the pmf?
>>
>>
>> Wei
>>
>>
>> <excerpt>hi wei,
>>
>>
>> you need to use the PMF routine at the same time to make this work.
>>
>>
>> -michael
>>
>>
>> On Oct 27, 2005, at 2:56 PM, Wei Zhuang wrote:
>>
>>
>> <excerpt>Hi,all:
>>
>>
>> I was trying to run a restrained-dihedralangle simulation, I put this
>>
>> paragraph in the .conf:
>>
>>
>> *****************************
>>
>> freeEnergy on
>>
>> freeEnergyConfig {
>>
>>
>> urestraint {
>>
>>
>> dihe (TRZ4,1,C) (TRZ4,2,N) ( TRZ4,2,CA) (TRZ4,2,C) barr=2000.0
>>
>> ref=-155.40
>>
>>
>> }
>>
>>
>> }
>>
>>
>> ********************************
>>
>>
>> the script went through with no problem, but when I checked the output
>>
>> pdb file, it seems like there is no constraint at all, could anybody
>>
>> give me some help about what is going on here?
>>
>>
>> Wei
>>
>>
>>
>>
>> </
>> excerpt>--------------------------------------------------------------
>> ----------
>>
>> --------------------------
>>
>> Michael Grabe, Ph.D.
>>
>> Post-doctoral Fellow
>>
>> Howard Hughes Medical Institute
>>
>> University of California, San Francisco
>>
>> 1550 4th Street GD482
>>
>> San Francisco, CA 94143
>>
>> mgrabe_at_itsa.ucsf.edu
>>
>> tel: ++ 415.476.4021
>>
>> http://itsa.ucsf.edu/~mgrabe
>>
>>
>>
>> hi wei,
>>
>>
>>
>> you need to use the PMF routine at the same time to make this work.
>>
>>
>>
>> -michael
>>
>>
>>
>> On Oct 27, 2005, at 2:56 PM, Wei Zhuang wrote:
>>
>>
>>
>> <<excerpt>Hi,all:
>>
>>
>>
>> I was trying to run a restrained-dihedralangle simulation, I put this
>>
>> paragraph in the .conf:
>>
>>
>>
>> *****************************
>>
>>
>> freeEnergy on
>>
>>
>> freeEnergyConfig {
>>
>>
>>
>> urestraint {
>>
>>
>>
>> dihe (TRZ4,1,C) (TRZ4,2,N) ( TRZ4,2,CA) (TRZ4,2,C) barr=2000.0
>>
>> ref=-155.40
>>
>>
>>
>> }
>>
>>
>>
>> }
>>
>>
>>
>> ********************************
>>
>>
>>
>> the script went through with no problem, but when I checked the output
>>
>> pdb file, it seems like there is no constraint at all, could anybody
>>
>> give me some help about what is going on here?
>>
>>
>>
>> Wei
>>
>>
>>
>>
>>
>> <</excerpt><<color><<param>0202,6969,1212<</
>> param>----------------------------------------------------------------
>> ----------------------------------<</color>
>>
>>
>> Michael Grabe, Ph.D.
>>
>>
>> Post-doctoral Fellow
>>
>>
>> <<color><<param>0202,6B6B,1212<</param>Howard Hughes Medical Institute
>>
>> <</color>
>>
>>
>> University of California, San Francisco
>>
>>
>> 1550 4th Street GD482
>>
>>
>> San Francisco, CA 94143
>>
>>
>> mgrabe_at_itsa.ucsf.edu
>>
>>
>> tel: ++ 415.476.4021
>>
>>
>> <<color><<param>0000,0000,FFFF<</param>http://itsa.ucsf.edu/
>> ~mgrabe<</color>
>>
>>
>>
>>
>> </excerpt>
>>
>> = = = = = = = = = = = = = = = = = = = =
>>
>>
>>
>>
>> <fontfamily><param>Hiragino Kaku Gothic Pro</param>$B!!!!!!!!!!!!!!!!CW(B
>>
>> $BNi!*(B
>>
>>
>> </fontfamily>
>>
>> <fontfamily><param>Hiragino Kaku Gothic
>> Pro</param>$B!!!!!!!!!!!!!!!!(B</fontfamily>Wei
>> Zhuang
>>
>> <fontfamily><param>Hiragino Kaku Gothic
>> Pro</param>$B!!!!!!!!!!!!!!!!(B</fontfamily>wzhuang_at_uci.edu
>>
>> <fontfamily><param>Hiragino Kaku Gothic
>> Pro</param>$B!!!!!!!!!!!!!!!!!!!!(B</fontfamily>2005-10-27
>>
>>
>>
>>
>>
>> </excerpt><color><param>0202,6969,1212</
>> param>----------------------------------------------------------------
>> ----------------------------------</color>
>>
>> Michael Grabe, Ph.D.
>>
>> Post-doctoral Fellow
>>
>> <color><param>0202,6B6B,1212</param>Howard Hughes Medical Institute
>> </color>
>>
>> University of California, San Francisco
>>
>> 1550 4th Street GD482
>>
>> San Francisco, CA 94143
>>
>> mgrabe_at_itsa.ucsf.edu
>>
>> tel: ++ 415.476.4021
>>
>> <color><param>0000,0000,FFFF</param>http://itsa.ucsf.edu/~mgrabe
>> color>
>>
>>
>>
>
> = = = = = = = = = = = = = = = = = = = =
>
>
> $B!!!!!!!!!!!!!!!!CW(B
> $BNi!*(B
>
>
> $B!!!!!!!!!!!!!!!!(BWei Zhuang
> $B!!!!!!!!!!!!!!!!(
Bwzhuang_at_uci.edu
> $B!!!!!!!!!!!!!!!!!!!!(B2005-10-27
>
>
>
>
------------------------------------------------------------------------
--------------------------
Michael Grabe, Ph.D.
Post-doctoral Fellow
Howard Hughes Medical Institute
University of California, San Francisco
1550 4th Street GD482
San Francisco, CA 94143
mgrabe_at_itsa.ucsf.edu
tel: ++ 415.476.4021
http://itsa.ucsf.edu/~mgrabe

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