Hello,
On Fri, Mar 12, 2010 at 3:40 PM, Denny Bromley
<dbromley.u.washington.edu> wrote:
> Thanks Dean. I'm trying VegaZZ and it seems pretty good.
>
> One of the things I was enjoying (in my naiveté) was the fragment library
> that comes with Avogadro - a couple of hundred fragments all ready to go.
> Do you know of another such library? Drawing all my molecules and residues
> by hand is going to get a little tedious (I'm a computer scientist by
> training so doing *anything* by hand rubs me the wrong way. :) )
A couple programs worth considering: DSVisualizer is a pretty good
program for this IMO. It has a ring-builder, though no fragment
library that you speak of. However, it is scriptable, which should
ease your CS side some. Another option is gabedit. This package is
more for creating input files for ab-initio packages (gaussian,
gamess, mopac, molcas, qchem, mpqc, and molpro I believe). However,
it has a drawing window where you can create structures, and it
includes a fairly extensive fragment library (but I don't know if it's
scriptable, and it's rather clunkier than DSVisualizer I think).
Right-clicking after you've built a structure in this window allows
you to save it as a PDB.
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.
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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 12 2010 - 13:30:02 PST
