[AMBER] Notes and warnings in the generalized Born calculation

From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Fri, 12 Oct 2012 14:24:45 -0400

Hi all,

I go the following notes and warnings in the output files (mdout) for the
generalized Born MD calculations.

Note: 1-4 EEL scale factors were NOT found in the topology file.
| Using default value of 1.2.

I need a suggestion on how to have those 1-4 EEL scale factors in the
.prmtop file. Would it have a big effect if I leave it as it is (with
default value of 1.2)?

| Note: 1-4 VDW scale factors were NOT found in the topology file.
| Using default value of 2.0.

I need a suggestion on how to have those 1-4 VDW scale factors in the
.prmtop file. Would it have a big effect if I leave it as it is (with
default value of 2.0)?


| WARNING: ATOMIC_NUMBER section not found. Guessing atomic numbers from
| masses for GB parameters. Remake topology file with AmberTools
12+
| or add atomic numbers with ParmEd to remove this warning.

Here, I would really appreciate a suggestion on how to add atomic numbers
using ParmEd.

Thank you

Sajeewa Dewage
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Received on Fri Oct 12 2012 - 11:30:03 PDT
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