i'm not sure why you say sander does not work- please explain what you did
and what the result is. you only specified for anal.
what are the "original" and "modified" versions?
2010/11/9 <Yokota_Akihiro.takeda.co.jp>
> ----------------------------
> Sorry to send a mail again.
> The title in my previous mail was blank.
> ----------------------------
>
> 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 - 04:30:03 PST
