Re: AMBER: ptraj questions

From: Carlos Simmerling <carlos.ilion.bio.sunysb.edu>
Date: Sun, 31 Oct 2004 10:45:21 -0500

I think nofit is broken, so overlap of 1 residue will always be small.

>The numbers I get are too small (around 0.05). The rmsd of CA is about
>1.2. So I suppose the rmsd of this sidechain should be around this
>number or larger.
>
>

you cannot mathematically define an overlap for less than 3 atoms.

>Another problem I have is when I choose less than three atoms of the
>sidechain, the program fails.
>
>Thanks for your help in advance.
>
>By the way, the ptraj program I have is ptraj-6.5.
>
>Best,
>Lishan
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Oct 31 2004 - 15:53:00 PST
Custom Search