Re: [AMBER] EM in vacuum

From: David A Case <>
Date: Wed, 3 Aug 2016 17:22:18 -0600

On Tue, Aug 02, 2016, Dmitry Suplatov wrote:
> I am trying to run an energy minimization in vacuum of my protein (400
> amino acids). The intention is to hopefully rebuild some hydrogen bonds in
> a particular loop. The orientation of some backbone atoms in this loop
> seems to be suboptimal, in a sense that they look like they could form
> H-bonds but the angles are not very good. As a result the loop collapses
> even after a short MD.
> So, my question. Below is my parameter file for performing EM in vacuum.
> The problem is - the atoms hardly move at all !!! The output coordinates
> are almost the same as the output ones. This does not feel right.

You might be close to a local minimum. Does the gradient norm (called "RMS"
in the output) go to a very low value? Does the energy change much? I think
you can appreciate that people on the mailing list probably cannot help much
if all they are told is that the results don't "feel right".

> Step-1: Minimize in vacuum only the water and ions, restraining the heavy
> atoms of protein and ligands at constant 3 kcal/mol-A^2

Note: the actual input file you provided doesn't match the above comment--i.e.
it doesn't contain any restraints.

> ncyc=2500, ! The method of minimization will be switched from SD to CG
> after ncyc cycles

This is a very large value for ncyc, but is just wasting computer time: the
second half of the minimization should still progress in the usual fashion.


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Received on Wed Aug 03 2016 - 16:30:03 PDT
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