[AMBER] "excluded atoms" declaration

From: <Yokota_Akihiro.takeda.co.jp>
Date: Tue, 9 Nov 2010 18:24:23 +0900

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Sorry to send a mail again.
The title in my previous mail was blank.
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Dear AMBER Users,

  I am studying the topology file of AMBER to modify it,
especially for "excluded atoms" declaration. And I found
a mysterious things below. Do you have any suggestions or
comments to me?

  Let me explain you in a simple case.

1. An original pdb file have only 2 water molecules, separated in 4A.
2. I changed the topology file, to ignore the nonbonded interactions
   between 2 water molecules.
   -> 3 points are modified(NEXT number in 8th line, %FLAG_NUMBER_EXCLUDEDATOMS,
      and %FLAG_EXCLUDED_ATOMS_LIST)
3. I checked the interaction energies of modified one by using Anal module.
   Anal said that nonbonded interaction between 2 waters is zero. This is OK.
4. And optimization by Sander module is performed, but the results from the
   original and the modified are definitely the same. Why does my
   "excluded atoms" declaration not work in Sander?
(This indicate that Anal module correctly recognizes the "excluded atoms"
 declaration in topology file, and the sander module does not.)

Do you have any suggestions or comments to me?

Thanks in advance,
Akihiro Yokota

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Received on Tue Nov 09 2010 - 01:30:05 PST
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