AMBER Archive (2009)

Subject: Re: [AMBER] restrained minimization

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon Apr 13 2009 - 21:03:11 CDT

On Mon, Apr 13, 2009, quantum_mania_at_yahoo.com wrote:
>
> I wanted to minimize a system with all heavy atoms frozen, so I had the input file:
>
> &cntrl
> ntxo = 1,
> ntf = 1, ntb = 0,
> cut = $13,
> imin = 1, maxcyc = 500,
> ncyc = 200, drms = 0.0001,
> igb = 2, gbsa = 1,
> saltcon= 0.2,
> ntr = 1, restraint_wt=100,
> restraintmask="!@H="
> &end

You can use the ambmask program to check out masks to make sure they are
doing what you want.

>
> The output, though, showed most atoms minimized were the heavy atoms:

?? I don't see how your output shows what you claim. Have you examined
the final coordinates themselves to see what moved? Note that you have
very bad contacts in the initial structure (very large VDW terms), so
you should expect some motion from heavy atoms, even with a very large
restraint weight.

...dac

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber