Re: Re: urestraint doesn't work

From: Wei Zhuang (wzhuang_at_uci.edu)
Date: Thu Oct 27 2005 - 20:35:22 CDT

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>
>
>
>

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

        崑

 
                                 
        Wei Zhuang
        
wzhuang_at_uci.edu
          2005-10-27

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