AMBER Archive (2006)

Subject: Re: AMBER: Format of the prmtop file (NUMBER_EXCLUDED_ATOMS) & (EXCLUDED_ATOMS_LIST)

From: David A. Case (
Date: Tue Nov 07 2006 - 19:51:48 CST

On Tue, Nov 07, 2006, Nitin Bhardwaj wrote:
> I have been trying to change the (NUMBER_EXCLUDED_ATOMS) &
> (EXCLUDED_ATOMS_LIST) fields in the prmtop file....
> of excluded atoms for the past two days. I have tried to read about
> the format of the prmtop file but I have not got it completely. I just
> have a few quick questions about the format of these two fields in the
> prmtop file.
> 1) if there are no excluded atoms for a particular atom, is it still
> specified as 1?

I believe this is correct, albeit pretty brain-dead.

> So, whenever, the next entry is smaller or equal to
> the previous one, it indicates that the list for a new atom has
> started.

I think you are supposed to use the "number_excluded_atoms" list to tell when
to move on to the next atom, and not rely on any relations in this list to
trigger that.

> 3) Does every row have to be 80 characters long with 10 entries (8
> characters for every entry that are aligned right-side)?.

yes. (I think)

Obviously, you will need to run some experiments, and/or study the code that
reads and uses these values, to be sure.

...good luck...dac

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