Date: Sat, 21 Jul 2001 13:15:13 -0700
From: David Case
Subject: Re: dissociation of protein from DNA in MD

On Sat, Jul 21, 2001, Michael Cooney wrote:

>
> I have started using iwrap=1 in simulations of solvated protein:DNA
> complexes, as has been suggested to keep all atoms in the same box image.
> However, after ~800 ps the DNA (16bp) still appears to dissociate from the
> peptide (66 aa). Is ptraj still needed to bring these noncovalently bonded
> components back into the same box?
>

Probably. The problem with iwrap=1 in sander is that it doesn't know
"how" to do the wrapping, i.e. which parts of the system to try to keep
together, etc. So for a simple system, (such as a single polypeptide chain)
iwrap=1 will often do the "right thing", but this is not guaranteed.
For systems with several solute chains (like 2 dna chains and 1 protein),
the algorithm sander uses may end up with the "wrong" unit cell locations.

We ptraj, you can tell the program how to wrap things to make it look
like what you want.

For this reason, I wanted to get rid of iwrap in sander, and do everything
in ptraj, but I got outvoted.

...good luck...dac