AMBER Archive (2009)

Subject: Re: [AMBER] zeros in excluded atom list in topology file

From: Peter Schmidtke (pschmidtke_at_mmb.pcb.ub.es)
Date: Fri Nov 06 2009 - 02:54:57 CST

On Thu, 5 Nov 2009 19:39:56 -0500, Carlos Simmerling
<carlos.simmerling_at_gmail.com> wrote:
> sorry if this is obvious, but are you sure you know how to read the
> exclusion list? it's a pointer for each atom, not an actual list.

Unfortunately by definition I am not sure about anything as documentation
is very sparse (else I wouldn't bother the mailing list with my very basic
questions ;)) about how to read an amber topology file. The way I
understand it is that in the topology file you have one list saying how
many excluded atoms you have for each atom. Next you have the excluded
atoms list, where you have, arranged from atom 1 to the end, all excluded
atoms.

So with an example it would be better :

%FLAG NUMBER_EXCLUDED_ATOMS
2 5 ....

This means I have two excluded atoms for atom 1, and 5 for atom 2
now if I want to know what these excluded atoms are, I have to go to the
excluded atom list :

%FLAG EXCLUDED_ATOMS_LIST
2 3 8 5 6 1 7

for giving a stupid example.

This means that for atom 1, atoms 2 and 3 are excluded, for atom 2 the
atoms 8,5,6,1 and 7 are excluded.

Apparently this is NOT the way I should read this, seen your question...but
in the end this is how I understand it.

Your question still, unfortunately does not point out how to interpret the
zeros in the excluded atom list. Is it because an interaction was already
excluded by a previous "role", so it is just redundant?

Thanks in advance.

Peter

>
> On Thu, Nov 5, 2009 at 12:06 PM, Peter Schmidtke
> <pschmidtke_at_mmb.pcb.ub.es>wrote:
>
>> Dear Amber Mailing list readers,
>>
>> I wondered why there were zeros in the excluded atom list in the amber
>> topology (parm) file of my system. I run simulations with explicit
>> solvent
>> and for example each water molecule has 2 (O), 1 (H), 1 (H) excluded
>> atoms
>> for calculating the non bonded interactions. But the single excluded
atom
>> for the second H atom points to atom 0 which does not exist, why?
>>
>> I saw also some zeros within the protein...why? Is this some amber
>> internal
>> coding saying that we have to do something special with this H atom,
like
>> a
>> 10-12 potential instead of the 6-12? If yes, what is done in the Coulomb
>> potential then?
>>
>> Thanks in advance for your reply.
>>
>> Best regards.
>>
>> --
>>
>> Peter Schmidtke
>>
>> ----------------------
>> PhD Student at the Molecular Modeling and Bioinformatics Group
>> Dep. Physical Chemistry
>> Faculty of Pharmacy
>> University of Barcelona
>>
>>
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-- 

Peter Schmidtke

----------------------
PhD Student at the Molecular Modeling and Bioinformatics Group
Dep. Physical Chemistry
Faculty of Pharmacy
University of Barcelona

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