In another context, I found the .ac type output best suited. I wanted
now to use antechamber in combination with charmmgen (I posted here
the query getting no answer but with much effort I solved the task)
and the only file format that worked perfectly well was the .ac. As
expected, .prepin files led to crash. Unexpectedly, also .mol2 files
from antechamber led to major errors with charmmgen. Must add that I
am at amber10, though not up-to-date with ambertools.
cheers
francesco pietra
On Sun, Mar 27, 2011 at 1:32 AM, case <case.biomaps.rutgers.edu> wrote:
> On Thu, Mar 24, 2011, thomas.fox.boehringer-ingelheim.com wrote:
>>
>> here is a simple example, methylene chloride:
>>
>> The pdb file is:
>> HETATM 1 C * 0 0.000 0.000 0.000 1.00 0.00 C
>> HETATM 2 CL * 0 1.773 0.000 0.000 1.00 0.00 CL
>> HETATM 3 H2 * 0 -0.363 0.727 0.727 1.00 0.00 H
>> HETATM 4 H3 * 0 -0.363 -0.993 0.266 1.00 0.00 H
>> HETATM 5 H4 * 0 -0.363 0.266 -0.993 1.00 0.00 H
>> CONECT 1 3 4 5 2
>> CONECT 2 1
>> CONECT 3 1
>> CONECT 4 1
>> CONECT 5 1
>> END
>>
>> The antechamber command:
>> antechamber -i test.pdb -fi pdb -o test.prepin -fo prepi
>>
>> As you can see, the IGRAPH in the prepin file for the chloride has been
>> changed from CL -> Cl.
>
> I can confirm that the current developer's code still has this problem. The
> problem goes away if the output format is mol2. (Another reason, among many,
> to avoid the prepi input if possible.)
>
> I'm cc-ing this to Junmei to see if he has any ideas.
>
> ...thanks for the report...dave
>
>
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Received on Sun Mar 27 2011 - 02:30:03 PDT
