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. :) )
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
>
>
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Received on Fri Mar 12 2010 - 13:00:02 PST
