Hi Stuart,
I've just copied over the new run I've just done into the trajectories
directory (with the name P450.) and run the top file through the new-to-old
converter, and originally named them P450_new.top and P450_old.top.
In the amber manual it does state that the format described is the 'old'
i.e. pre-amber7 format.
Ian
Stuart Murdock wrote:
> 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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--
Dr. Ian Withers Tel: +44 (0)115 8468009
Centre for Biomolecular Science,
University of Nottingham, email: ianw.holmes.cancres.nottingham.ac.uk
Nottingham, NG7 2RD, UK. http://holmes.cancres.nottingham.ac.uk/mrg/ianw/
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Received on Tue Feb 15 2005 - 13:53:00 PST
