Hi all,
Problem solved with -pl 15. Thank you.
Maura Malinska
On 04/12/2017 06:54 PM, Niel Henriksen wrote:
>>> But then multitude of lines like this shows up and program stops:
>>> Info: the number of the path atoms exceeds MAXPATHATOMNUM(145000) for
>>> atom[32],extend the size and reallocate the memory automatically
>> I can confirm the problem. Antechamber runs fine if you don't ask for
>> bcc charges, but gets lost in the cyclic molecule in assigning bond types
>> during the bcc procedure.
>>
>> Not sure if any the SAMPL5 folks have run across this. I'm looking for a
>> workaround, and will post anything I find here.
>>
> Yeah, we see this with multi-cyclic residues like CB6/CB7. Antechamber has
> a maximum path length setting (see the -pl command) to help with this. Try
> setting it to something like "-pl 15". My understanding is that this will
> prevent antechamber from continuing to search for equivalent atoms beyond
> 15 bond lengths, which should be fine. As Dave indicated, without this
> setting it will continue the search by circling around the molecule,
> probably infinitely.
>
> Best,
> --Niel
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--
********************************************************
Maura Malinska, Ph.D.
Senior Research Associate
mmalinska.chem.uw.edu.pl
Faculty of Chemistry, University of Warsaw
Pasteura 1, 02-093 Warsaw, Poland
+48 22 552 63 56
http://crystal.chem.uw.edu.pl/
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Received on Thu Apr 13 2017 - 00:30:02 PDT
