Hi Alan,
The different file exists because the original file (file in
directory
amber10/dat/leap/parm) has some minor problems
For example, in parm99.dat there is the following improper torsion:
X -X -CA-H5 1.1 180. 2.
However, there is no parameter for bond CA-H5, which means this
entry will never be referenced.
tleap/xleap will ignore these entries, but sleap cannot ignore
them
it will stop for the error. Therefore I created other files in the
directory
amber10/dat/leap/gleap. which does not contain there entries.
Since the files just differ by some entries which will never be
used,
it will not affect the resulted topology file.
However, it is still a problem. I am working on now, and the new
release of AmberTools will only have one set of parameter files.
Sincerely,
Wei
On Apr 12, 2009, at 4:30 AM, Alan wrote:
> Hi list,
>
> I would like to understand why we have parm99.dat, gaff.dat etc. in
> two different folders in amber10 distribution (amber10/dat/leap/gleap/
> and amber10/dat/leap/parm) and, more intriguing, why e.g. parm99.dat
> and gaff.dat are different in these folders!
>
> Methinks this is prone for mistakes and sometimes I think I saw things
> related to gaff missing parameters between amber releases in this
> list.
>
> Cheers,
>
> Alan
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>> http://www.bio.cam.ac.uk/~awd28<<
>
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Received on Mon Apr 13 2009 - 01:08:09 PDT
