> From: Jason Swails <jason.swails.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Date: Fri, 12 Mar 2010 15:16:56 -0600
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Antechamber question: all my residue carbons are the same
> 'c3' atom type.
>
> Both programs are free (only gabedit is open source), though neither
> has a Mac version that I know of (but you can build wine from macports
> and run them that way). Both can be installed on Windows, and I use
> both on Linux, so Mac is the only option left out.
>
Just my 2cents here. gabedit runs fine on MacOS X11.
DSVisualizer requires high level graphics ability, and I don't know
if wine emulates that or not. For example, DSVisualizer graphics are
are not usable (way too slow) using Parallels versions that do not support
graphics acceleration, but ver5 and maybe 4 does.
Dean
Dr. Dean Cuebas, Associate Professor of Chemistry
deancuebas.missouristate.edu,
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897
> Hope this helps,
> Jason
>
>>
>> Anyway, thanks for the help! I really appreciate it-
>>
>> -denny-
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> -----Original Message-----
>> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf
>> Of Dean Cuebas
>> Sent: Friday, March 12, 2010 10:07 AM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] Antechamber question: all my residue carbons are the
>> same 'c3' atom type.
>>
>> Hello
>>
>>> From: Denny Bromley <dbromley.u.washington.edu>
>>> Reply-To: AMBER Mailing List <amber.ambermd.org>
>>> Date: Fri, 12 Mar 2010 11:50:27 -0600
>>> To: AMBER Mailing List <amber.ambermd.org>
>>> Cc: "dbromley.u.washington.edu" <dbromley.u.washington.edu>
>>> Subject: RE: [AMBER] Antechamber question: all my residue carbons are the
>> same
>>> 'c3' atom type.
>>>
>>> Thanks for the tip. I ran the ash pdb using my same command line and it
>>> does look better ('c' and 'c3' now which makes more sense at least.) The
>>> text from my input pdb is below although I'm busy looking into new tools
>>> thanks to heads up from Dean.
>>>
>>> Thank you for both for the quick responses,
>>> -denny-
>>>
>>>
>>>
>>> //benzene saved out from avogadro
>>> COMPND UNNAMED
>>> AUTHOR GENERATED BY OPEN BABEL 2.2.3
>>
>>
>>
>>> H
>>> CONECT 1 2 2 6 7
>>> CONECT 2 1 1 3 8
>>> CONECT 3 2 4 4 9
>>> CONECT 4 3 3 5 10
>>> CONECT 5 4 6 6 11
>>> CONECT 6 5 5 1 12
>> ^ ^
>> .
>> .
>> .
>>
>> Note the incorrect atoms connected to themselves conect record.
>>
>> Below is the correct way
>>
>> CONECT 1 2 6 7
>> CONECT 2 1 3 8
>> CONECT 3 2 4 9
>> CONECT 4 3 5 10
>> CONECT 5 4 6 11
>> CONECT 6 5 1 12
>> .
>> .
>> .
>>
>> Also, I forgot to mention that I use MarvinSketch for drawing structures on
>> the Mac, also free. Just stay away from Avogadro until maybe it's been
>> around a few years more...
>>
>> Hope this helps,
>>
>> Dean
>>
>>> -----Original Message-----
>>> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
>> Behalf
>>> Of case
>>> Sent: Friday, March 12, 2010 4:47 AM
>>> To: AMBER Mailing List
>>> Subject: Re: [AMBER] Antechamber question: all my residue carbons are the
>>> same 'c3' atom type.
>>>
>>> On Thu, Mar 11, 2010, Denny Bromley wrote:
>>>>
>>>> My amino acid PDB files were from the Avogadro fragment library and
>>> exported
>>>> via Avogadro into the PDB format.
>>>
>>> It would help if you could post one of the input pdb files. You could
>>> look at the test case in $AMBERHOME/test/antechamber/ash, where an
>> aspartic
>>> acid molecule is handled, and not all carbon atoms are c3. Try to figure
>>> out
>>> what is different from your input and that one. A similar example is in
>>> the ../guanine_amber directory. [I'm assuming all the test cases pass, or
>>> you
>>> would have said something.]
>>>
>>> ....dac
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>> _______________________________________________
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>>
>>
>>
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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 Fri Mar 12 2010 - 15:00:02 PST
