Re: Applying conformational constraints during simulation

From: Victor Ovchinnikov (ovchinnv_at_MIT.EDU)
Date: Mon Oct 22 2007 - 23:21:09 CDT


The TMD function in NAMD should be able to do exactly this. See the
user's guide on pages 72-73. A word of caution: when run in parallel,
some NAMD binaries give errors in TMD. There are posts on this problem
on this list. I do not know whether this issue has been resolved yet.

I'm not sure what you mean by your second question. Could you clarify?


On Tue, 2007-10-23 at 13:08 +1000, wrote:
> I have a protein which I am pulling from a binding site by SMD (center of
> mass coordinates). In order to keep the protein properly folded I am
> planning on applying a coordinate-based constraint based on aligning its
> backbone reference to the protein's current position in the system.
> Is this possible in NAMD? There's an equivalent process in the latest
> CHARMM (recorded in cons.doc under RMSD constraints) - is there a way to
> align a reference set of coordinates during the simulation?
> ---
> Also, is it possible to freeze the coordinates of the ligand and still move
> it during simulation?
> Poker.
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:24 CST