AMBER Archive (2006)

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

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Tue Nov 07 2006 - 15:08:42 CST

Dear Amber community,

  I have been trying to change the (NUMBER_EXCLUDED_ATOMS) &
(EXCLUDED_ATOMS_LIST) fields in the prmtop file to create my own set
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.

NUMBER_EXCLUDED_ATOMS:
1) if there are no excluded atoms for a particular atom, is it still
specified as 1? I have seen a few examples where there were no
excluded atoms listed in the list of exlcuded atoms for these atoms
(there was just a single 0) but still the count under
NUMBER_EXCLUDED_ATOMS was 1 for these atoms.

EXCLUDED_ATOMS_LIST
1) Just want to make sure that I got the format right. We keep listing
the excluded atoms for each atom in succession. So, for the first atom
(atom # 1) we list, say,
2 3 4 5 6. And then we list for atom # 2, say, 3 4
5 6 7 8. So, whenever, the next entry is smaller or equal to
the previous one, it indicates that the list for a new atom has
started.

2)When there are no excluded atoms for a particular atom, we just list
0 for that atom.

3) Does every row have to be 80 characters long with 10 entries (8
characters for every entry that are aligned right-side)?. Will amber
not read it properly if a row is only 64 characters long with only 8
entries and then continues in the next line?

4) Are NUMBER_EXCLUDED_ATOMS & EXCLUDED_ATOMS_LIST the only two
fields that I need to change my set of excluded atoms?

Thanks a lot in advance,
Rgds,
Nitin
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