Re: [AMBER] (no subject)

From: Jason Swails <>
Date: Tue, 9 Nov 2010 11:26:41 -0500

On Tue, Nov 9, 2010 at 4:19 AM, <> wrote:

> 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,

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.)

You don't give enough information here. How exactly did you modify
NUMBER_EXCLUDED_ATOMS and EXCLUDED_ATOMS_LIST? Do you know what the numbers
in each section mean (including the ordering)? Furthermore, if you want to
adjust the number of excluded atoms, you will probably have to adjust at
least one of the pointer values in the first section (%FLAG POINTERS).
 Sander does recognize excluded atoms, which is why a simulation of a free
O2 will have no non-bonded energy contributions, so there has to be
something in your setup that is not quite correct. Keep in mind that the
prmtop is not intended to be modified by hand, and great care is needed when
you try this. In this case, it is very helpful to consult the source code.

For instance, look at the rdparm.f file, where it reads the
EXCLUDED_ATOMS_LIST (search for that phrase). It will only read in the
first "nnb" terms. Therefore, even if you added more terms to this list,
unless you also changed the nnb pointer (NEXT according to the amber file
formats, or the 11th pointer in the POINTERS block), sander will not use

Hope this helps,

Do you have any suggestions or comments to me?
> Thanks in advance,
> Akihiro Yokota
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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Tue Nov 09 2010 - 08:30:03 PST
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