Re: [AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type.

From: Dean Cuebas <deancuebas.missouristate.edu>
Date: Fri, 12 Mar 2010 11:39:54 -0600

Hi Denny,

Avoid Avogadro! It is not a "research level" app and it is only at version
1 and still has MANY bugs that will drive you nuts, and I know for a fact it
produces incorrect CONECT records almost all the time.

Try Chimera, Yasara Viewer, or DeepView(Swiss PDBViewer) for the Mac.

Personally, I use VegaZZ most of the time under Parallels.

All the above are free.

Hope this helps.

Dean

-- 
Dr. Dean Cuebas, Associate Prof of Chemistry
deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897
> From: case <case.biomaps.rutgers.edu>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Date: Fri, 12 Mar 2010 06:47:28 -0600
> To: AMBER Mailing List <amber.ambermd.org>
> 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

Received on Fri Mar 12 2010 - 10:00:02 PST