Re: [AMBER] Using restraints to get a complex

From: David A Case <>
Date: Fri, 9 Jan 2015 08:06:56 -0500

On Fri, Jan 09, 2015, wrote:

> Thanks for the suggestions. What I meant by "nothing happens" is
> that the simulation with or without the EMAP constraints resulted in
> secondary structure being completely destroyed. When I checked my
> trajectory output, the emap energies were given as 0.

> Since then, I've checked the test files, and have used the input file
> from the emap2 test as a basis for mine (see below). This results in
> EMAP values of around -4500, which sounds much better.


> The main difference between the two systems, I think, is that
> I wasn't originally using SG-langevin dynamics (only langevin
> thermostatization).

Are you sure that the only difference between getting EMAP of 0 and -4500
is the presence of isgld=1, and the everything else is absolutely identical?
I don't have easy accss to your earlier email, but I think you used a blank
for mapfile, and maybe had some other changes from what you have here.

The use of self-guided dynamics should be indenpendent of emap constraints.


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Received on Fri Jan 09 2015 - 05:30:02 PST
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