Hi Tom,
On 9/01/2012, at 1:15 PM, Thomas Pochapsky wrote:
> I am new to antechamber, I am trying to parameterize a macrocyclic compound, and am unable to get atom types or even coordinates in my output files, even using the sustiva_h.pdb tutorial example. It looks like a path problem to me, but Amber runs OK, so should I have additional lines in my .cshrc so that antechamber finds the parameters it is looking for?
>
> I am providing the input line I used from the tutorial, and the output.
>
> input:> antechamber -i sustiva_h-1.pdb -fi pdb -o sustiva_h.mol2 -fo mol2 -c bcc -s 2
>
> output:
> Running: /nmr/Programs/amber/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
>
> Total number of electrons: 160; net charge: 0
>
> Running: /nmr/Programs/amber/amber8/exe/divcon
>
> Running: /nmr/Programs/amber/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /nmr/Programs/amber/amber8/dat/antechamber/BCCPARM.DAT -j 4
>
> Cannot successfully assign bond type for this molecule, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase MAXVASTATE in define.h and recompile bondtype.C
I see you're still using Amber 8. Antechamber has been re-released a number of times since then, now as part of AmberTools, a free download from
http://ambermd.org. You may wish to download AmberTools 1.5 (the most recent version) and try its antechamber.
Regards,
Ben
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Received on Mon Jan 09 2012 - 10:30:05 PST
