AMBER Archive (2009)

Subject: Re: [AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm

From: Alan (alanwilter_at_gmail.com)
Date: Sun Apr 12 2009 - 10:58:18 CDT

Many thanks dear Wei!

Really great to know this.

With the next release, I'll give sleap a nice try in our ligands DB here.

Cheers,
Alan

On Sun, Apr 12, 2009 at 14:24, Wei Zhang <zgjzweig_at_gmail.com> wrote:
> 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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>
>
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-- 
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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