On Wed, Jan 01, 2014, Jonathan Saboury wrote:
> > Can you provide more information? What makes you think that sqm ran out
> of
> > memory? Why at atom 65?
>
> In the included I/O file (nohup.out) shows the console output. At the end
> of the file there is:
> ~~~
> Info: the number of the path atoms exceeds MAXPATHATOMNUM(2480000) for
> atom[65],extend the size and reallocate the memory automatically
> Info: the number of the path atoms exceeds MAXPATHATOMNUM(2485000) for
> atom[65],extendKilled
> ~~~
These messages don't come from sqm at all, but from antechamber. Furthermore,
they are not errors, just informative messages.
>
> Here is the .pdb: http://pastebin.com/raw.php?i=bP2Dfd3Z
You molecule really has only three types of atoms: alkanes, carboxylic acids,
and ethers. Amber has parameters for the first two (since they are in
proteins), and you can find or generate parameters for ethers (say by looking
at dimethyl ether). Then either by hand, or by writing a little script, you
can assign atom types and charges to all the atoms in your molecule. (I would
create a mol2 file, and just edit that, since the places where charges and
atom types go are pretty clear.) Then you can load your modified mol2 file
directly into LEaP.
Note: your molecule has protonated versions of the acids. This may not be
what you want, if you are thinking of running simulations in water.
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 02 2014 - 05:30:02 PST
