AMBER Archive (2003)

Subject: AMBER: prmtop file format

From: Herbert Georg (hcgeorg_at_if.usp.br)
Date: Fri Oct 24 2003 - 09:37:42 CDT

I was taking a look at the prmtop file format description in the amber7 manual
and in the amber site but it seems that my prmtop file doesn't match the
description. It seems that some new flags were added and the format of the flags
has changed. Could someone help me out with this new format?
For example, in the flag BONDS CONTAINING HYDROGEN the manual and the site have
the following description:

FORMAT(12I6) (IBH(i),JBH(i),ICBH(i), i=1,NBONH)
   IBH : atom involved in bond "i", bond contains hydrogen
   JBH : atom involved in bond "i", bond contains hydrogen
   ICBH : index into parameter arrays RK and REQ

and my prmtop file has the following for that flag:

%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
        0 3 1 6 9 1 18 21 5 18
       24 5 18 27 5 30 33 5 30 36
        5 30 39 5 42 45 1 48 51 1
       57 60 7 63 66 7 69 72 10

According to the description above, there is an atom numbered 'zero'.
Furthermore, there are atoms numbered above 26 which is the total number of atoms.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu