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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Received on Mon Feb 07 2011 - 02:00:04 PST
