AMBER Archive (2003)

Subject: Re: average structure generated by carnal

From: Peter Gannett (pgannett_at_hsc.wvu.edu)
Date: Tue Jan 21 2003 - 14:14:38 CST

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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