AMBER Archive (2005)

Subject: AMBER: Topology Format Amber 8

From: Stuart Murdock (s.e.murdock_at_soton.ac.uk)
Date: Tue Feb 15 2005 - 06:00:56 CST

Hi

I am trying to write an Amber (8) file parser to get all the information
from the topology and output files which will run automatically to
archive my trajectories. I want this to work on many Amber simulations
which are performed in my wider community but I am having trouble with
quite different formats.

On the web page and in the Amber 8 manual (apart from the %'s ) we have
the format for the top file as

FORMAT(20a4) (ITITL(i), i=1,20)
FORMAT(12i6) NATOM, NTYPES ....... ......
FORMAT(20a4) (IGRAPH(i), i=1,NATOM)
FORMAT(5E16.8) (CHRG(i), i=1,NATOM)
FORMAT(5E16.8) (AMASS(i), i=1,NATOM)
FORMAT(12I6) (IAC(i), i=1,NATOM)
FORMAT(12I6) (NUMEX(i), i=1,NATOM)
FORMAT(12I6) (ICO(i), i=1,NTYPES*NTYPES)
FORMAT(20A4) (LABRES(i), i=1,NRES)
FORMAT(12I6) (IPRES(i), i=1,NRES)
FORMAT(5E16.8) (RK(i), i=1,NUMBND)
FORMAT(5E16.8) (REQ(i), i=1,NUMBND)
FORMAT(5E16.8) (TK(i), i=1,NUMANG)
FORMAT(5E16.8) (TEQ(i), i=1,NUMANG)
FORMAT(5E16.8) (PK(i), i=1,NPTRA)
FORMAT(5E16.8) (PN(i), i=1,NPTRA)
FORMAT(5E16.8) (PHASE(i), i=1,NPTRA)
FORMAT(5E16.8) (SOLTY(i), i=1,NATYP)
FORMAT(5E16.8) (CN1(i), i=1,NTYPES*(NTYPES+1)/2)
FORMAT(5E16.8) (CN2(i), i=1,NTYPES*(NTYPES+1)/2)

.... etc.

But one of my collegues is using what he thinks to be standard Amber 8
and this top file has the following format. Does anyone have any ideas
as to why there is a difference?

FORMAT(20a4)
FORMAT(10I8)
FORMAT(20a4)
FORMAT(5E16.8)
FORMAT(5E16.8)
FORMAT(10I8)
FORMAT(10I8)
FORMAT(10I8)
FORMAT(20a4)
FORMAT(10I8)
FORMAT(5E16.8)
FORMAT(5E16.8)
FORMAT(5E16.8)
FORMAT(5E16.8)
FORMAT(5E16.8)
FORMAT(5E16.8)
FORMAT(5E16.8)
FORMAT(5E16.8)
FORMAT(5E16.8)
FORMAT(5E16.8)

.... etc.

Thanks

Stuart

Stuart Murdock Ph.D,
Research Fellow,
Dept. of Chemistry / E-Science,
University of Southampton,
Highfield, Southampton,
SO17 1BJ, United Kingdom
 
http://www.biosimgrid.org

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