do you have restraints on during the run? if the structure rotates at all,
the image/center won't be giving you a good overlap of the structures and I
would expect the average command to give you unreasonable results. you
might want to add some fitting to your script.
sorry that doesn't answer your question, but I wanted to point it out.
On Mon, Feb 15, 2016 at 11:42 AM, Michael Shokhen <michael.shokhen.biu.ac.il
> wrote:
> Dear Amber list experts,
>
>
> I use a standard cpptraj scipt for the generation of the average 3D
> structure of
>
> receptor - ligand complex:
>
>
> parm ../mc.prmtop
> trajin ../5_/mc_md3.mdcrd
> trajin ../6_/mc_md4.mdcrd
> trajin ../7_/mc_md5.mdcrd
> trajin ../8_/mc_md6.mdcrd
> trajin ../9_/mc_md7.mdcrd
> trajin ../10_/mc_md8.mdcrd
> strip :WAT
> strip :Cl-
> center :1-508 mass origin
> image origin center familiar
> average av_md3-8.pdb PDB
> run
> quit
>
>
> My question is: How to modify the cpptraj script in order to collect
> for the averaging only that MD frames
>
> where the interatomic distance:
>
>
> distance R5_E89 :5.67 :89.1503
>
> belongs to the interval from 3 to 5 A?
>
>
> Many thanks,
>
> Michael
>
>
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: shokhen.mail.biu.ac.il<
> https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il
> >
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Received on Mon Feb 15 2016 - 09:00:07 PST
