Re: Re: urestraint doesn't work

From: Wei Zhuang (wzhuang_at_uci.edu)
Date: Thu Oct 27 2005 - 21:45:37 CDT

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>
>>>
>>>
>>>
>>
>> = = = = = = = = = = = = = = = = = = = =
>>
>>
>>         崑
>> 撰
>>
>>
>>         Wei Zhuang
>>         
wzhuang_at_uci.edu
>>           2005-10-27
>>
>>
>>
>>
>------------------------------------------------------------------------
>--------------------------
>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<>
>
>
>
>
></excerpt>
>
>= = = = = = = = = = = = = = = = = = = =
>
>
>
>
><fontfamily><param>Hiragino Kaku Gothic Pro</param>        崑
>
>撰
>
>
> </fontfamily>
>
><fontfamily><param>Hiragino Kaku Gothic Pro</param>        </fontfamily>Wei
>Zhuang
>
><fontfamily><param>Hiragino Kaku Gothic Pro</param>        </fontfamily>
wzhuang_at_uci.edu
>
><fontfamily><param>Hiragino Kaku Gothic Pro</param>          </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>
>
>
>

= = = = = = = = = = = = = = = = = = = =
                        

        崑

 
                                 
        Wei Zhuang
        
wzhuang_at_uci.edu
          2005-10-27

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