AMBER Archive (2004)

Subject: AMBER: Dummy torsion paramters for thermodynamic integration

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Tue Dec 21 2004 - 02:25:31 CST

Dear Amber users,

when I prepare a system for thermodynamic integration
calculations in leap, saveaberparmpert gives me lines like
the following for proper and improper torsion parameters:

-----
*** Improper torsion parameters missing ***
atom names: C6-H8-C8-H9
atom types: c2-hc-c3-hc =pert=> ce-hc-c3-hc
Please add a dummy parameter of multiplicity 2 for the pert
types to your parameter set.
- e.g. ce-hc-c3-hc 0.0 0. 2.
(This is because multiple torsional potentials may apply to
a single torsion, and each is perturbed individually in
gibbs.)
-----

My questions are:

Is this error still relevant if I perform my TI runs with
sander instead off gibbs? If not can I turn it off to be
able to write my top files without these lines?

When I add the dummy parameters requested, even after
removing duplicate ones, ca. 30 entries remain for my
.frcmod file. When I load these, I get another warning:

-----
WARNING: expected Improper Torsion PK>0 (0.000000)
WARNING: expected Improper Torsion PHASE=180 (0.000000)
Here is the Improper Torsion line in question:
cd c ce c3 0.0 0. 2. as requested by leap
-----

Does this warning only appear because it is a dummy
improper term or do I have to change something?

Thanks for your time,

Kind regards,

Thomas

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