Another thought -- the error message suggests that the gaussian simulation
may have not have finished successfully (which is the primary reason I
suggested you send the output file instead of the input file). You may be
able to check this yourself by trying to open your output file with another
program that parses gaussian outputs (i.e. gaussview, gausssum, gabedit,
openbabel, etc.) and see if they have a problem with it as well. That may
save you the hassle of sending us the output file only to be told something
you could figure out that way (another quick check is that gaussian
typically has a random quote at the end of the output file with some kind of
line about successful completion if it has in fact finished properly -- this
would be a good thing to look for.
Good luck!
Jason
On Wed, May 26, 2010 at 1:21 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> If all you're trying to do is convert a gaussian output file to a PDB, may
> I suggest using openbabel instead. If you are trying to create a custom
> residue library for use in leap (or amber), then I would suggest choosing
> some format with charges (i.e. amber prep or mol2 file). See the tutorials
> on how to appropriately use a gaussian output file to obtain this (
> ambermd.org/tutorials/).
>
> On the other hand, providing us with the gaussian output file as opposed to
> the input file would help diagnosing the issue, too (unless someone more
> knowledgeable than me can see something wrong with the command straight away
> and comment).
>
> All the best,
> Jason
>
> 2010/5/26 <missing_grace.sina.com>
>
>> Hi, i try to use antechamber to convert the Gaussian output file
>> (1G5Q.log) to the pdb format ,use it : antechamber -i 1G5Q.log -fi gout -o
>> 1G5Q.pdb -fo pdb
>> But i always the line:No atom read in, the gaussian output file may not
>> complete, exit
>> i do not know what is wrong
>> Could you give me some help ?
>> Thank u in advance !
>>
>> Check the Guassian input file and the pdb file.
>>
>> _______________________________________________
>> 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue May 25 2010 - 22:30:07 PDT
