AMBER Archive (2005)

Subject: AMBER: Protein With Structural Ions

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Tue Apr 12 2005 - 12:47:52 CDT

I haven't seen my reply post, so I'm sending it again.

Kara

Would I only include the &wt type="end" portion? If I don't have any
&wt, it won't run through sander.

When I look at the output, it says that it read in the restraints:

------------------------------------------------------------------------
------
    3. ATOMIC COORDINATES AND VELOCITIES
------------------------------------------------------------------------
--------

  begin time read from input coords = 0.000 ps

            Begin reading energy term weight changes/NMR restraints
  WEIGHT CHANGES:
  REST 0 10000 1.000000 1.000000 0 0

  RESTRAINTS:
  Requested file redirections:
   DISANG = enzph1alarestraints.f
  Restraints will be read from file: enzph1alarestraints.f
  Here are comments from the DISANG input file:
  # distance restraints prepared by hand for Ca
  #( oxygen 1 Calcium upper bound)
  #
  # 79 GLY O 171 CA CA 2.8
  #

                        Number of restraints read = 4

                   Done reading weight changes/NMR restraints

But each step says the following:

  NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
0.000

Did I set something incorrectly? It doesn't look like it's actually
restraining anything.

Thanks,

Kara Di Giorgio

On Apr 12, 2005, at 9:09 AM, Carlos Simmerling wrote:

> I don't think you need to use the weight change on REST if it isn't
> changing.
>
> look at the output file- does it properly read the restraints? when
> the Ca moves,
> does the restraint energy change? read the output carefully, it should
> tell you what's going on.

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