---------- Forwarded message ----------
From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Fri, Oct 12, 2012 at 2:24 PM
Subject: Notes and warnings in the generalized Born calculation
To: AMBER Mailing List <amber.ambermd.org>
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 - 14:30:02 PDT
