the whole point of the new format in amber8 is that the things you list
(ie the actual format statements for each set of data) are specified
in the prmtop file itself. your parser will have to read the file to
get the format, and then read the data. Take a look at the file itself -
if you've got the ability to write a parser, the file should be pretty
much self-explanatory compared to the older prmtop format. You might
also take a look at the Amber code that reads it for some ideas.
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
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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Received on Tue Feb 15 2005 - 12:53:00 PST
