I believe it's now just free-format, whitespace-delimited now. The file
format page is *very* old (predating amber7 by a good bit I'd wager since I
only just updated the prmtop section for the parm7 file format). My
suggestion is to just remove the format statements altogether, as I don't
think any kind of fixed formatting is used there anymore (and at the very
least it's not even followed).
All the best,
Jason
On Mon, Feb 7, 2011 at 4:36 AM, Mark <mjw.mjw.name> wrote:
>
> Dear all,
>
> A colleague has been asking me some questions about the parm.dat file
> format
> within the context of parsing and he has noticed an issue. The input for
> card 2,
> atom symbols and masses (see http://ambermd.org/formats.html#parm.dat ) is
> FORMAT(A2,2X,F10.2x,f10.2), however, if you look at either parm9{4,9}.dat,
> the
> formatting for this is (~ == one space):
>
> C~~12.01~~~~~~~~~0.616~~!~~~~~~~~~~~~sp2~C~carbonyl~group~
> CA~12.01~~~~~~~~~0.360~~~~~~~~~~~~~~~sp2~C~pure~aromatic~(benzene)
>
> There is only one space after the atom type and hence the format appears to
> be
> FORMAT(A2,1X,F10.2x,f10.2). A second issue appears in card 8:
>
> HW OW 0000. 0000. 4. flag for fast
> water
>
> This does not parse against:
>
> FORMAT(2X,A2,2X,A2,2x,5F10.2,I2) KT1,KT2,A,B,ASOLN,BSOLN,HCUT,IC ; 'flag'
> should be 1 char right
>
> I know these may seem like a minor issues since within the AMBER "workflow"
> these files are generally used as intermediate which are only parsed by C
> tools
> and work because the tool does not actually use FORTRAN format definitions
> (sscanf() is used instead). However, if there is a format definition by us,
> then
> it should actually be correct. So, are these errors in
> http://ambermd.org/formats.html#parm.dat documentation or typos in the
> parm.dat
> files?
>
> Regards,
>
> Mark
>
> _______________________________________________
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> AMBER-Developers.ambermd.org
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Feb 07 2011 - 07:00:04 PST
