AMBER Archive (2003)

Subject: RE: average structure generated by carnal

From: Kristina Furse (kristina.e.furse_at_vanderbilt.edu)
Date: Tue Jan 21 2003 - 19:55:46 CST

You could run a quick minimization on the average structure. That should pop
the bondlengths back to normal, but could introduce other distortions. Big
distortions in an average structure mean a lot of motion in the simulation
(ideally if this motion is around an equilibrium structure, the average should
look OK), so if it looks that bad, it might be that your system is not
equilibrated and an average structure is not appropriate.

Good luck!

Kristina

>===== Original Message From eric hu <erichu_linux_at_yahoo.com> =====
>I don't happen to have moil-view installed. Is there
>another way to do this with simple amber commands?
>
>Eric
>--- Peter Gannett <pgannett_at_hsc.wvu.edu> wrote:
>> Eric:
>>
>> I am certainly not the expert on this. However, I
>> have run into this problem. Average structures from
>> an MD run are just that and can lead to the weird
>> things you mention and others - like flat
>> deoxyribose rings. Rather than an average
>> structure, perhaps a 'most representative structure'
>> would suit your needs better. This can be obtained
>> using the cluster analysis option of Moil-View.
>>
>> Hope this helps.
>>
>> Pete Gannett
>>
>>
>> >>> eric hu <erichu_linux_at_yahoo.com> 01/21/03
>> 01:53PM >>>
>> Hi, I use carnal to generate an average pdb file
>> from
>> the trajectory. It seems to me that the new
>> structure
>> looks a little bit weird. Some C-H bonds are
>> extremely
>> short while C-N bonds are ridiculous large. These
>> happen on both the substrate and the protein. I
>> wonder
>> if people ever run into the similar situation. By
>> the
>> way I use antechamber to generate the force
>> parameter
>> for my substrate.
>>
>> Eric
>>
>>
>> # carnal.in--generate average pdb file
>> FILES_IN
>> PARM p1 ./4bound.top;
>> STREAM s1 ./TS4_md2.mdcrd.gz;
>> FILES_OUT
>> COORD c1 ./TS4_1ns.pdb PDB;
>> DECLARE
>> OUTPUT
>> COORD c1 s1 AVERAGE;
>> END
>>
>>
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>
>
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****************************************************
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
email: kfurse_at_structbio.vanderbilt.edu