Re: [AMBER] Antechamber for PCBM

From: soukaina louerdi <s.louerdi.uhp.ac.ma>
Date: Fri, 23 Nov 2018 23:12:04 +0100

Dear Pr.Malinska,
Thanks for your reply and your Help
I will do it.

With Regards.


Le ven. 23 nov. 2018 à 18:01, Maura Malinska <mmalinska.chem.uw.edu.pl> a
écrit :

> Hi,
>
> Try to add to your command: -pl 15
>
> It has problem with cyclic molecules.
>
> Hope it helps.
>
> --
> Maura Malinska
> Assistant Professor
> Faculty of Chemistry
> University of Warsaw
> ul. Ludwika Pasteura 1, 02-093 Warsaw, Poland
>
> tel. 22 55 26 356
> mmalinska.chem.uw.edu.pl
>
> www.uw.edu.pl,
> http://crystal.chem.uw.edu.pl/staff/malinska.html
>
> On 11/23/18 4:37 PM, soukaina louerdi wrote:
> > Dear Pr.Case
> >
> > Many Thanks to your email.
> > I tried to do example C60 ( AmberTools\test\antechamber ) :
> >
> > $AMBERHOME/bin/antechamber -i buckyball.pdb -fi pdb -o buckyball.mol2 -fo
> > mol2
> >
> > I get the file mol2.
> > But when I add " -c bcc -s 2 " :
> >
> > $AMBERHOME/bin/antechamber -i buckyball.pdb -fi pdb -o buckyball.mol2 -fo
> > mol2 -c bcc -s 2
> >
> > I found the following informations :
> > Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (
> > ID:0, Name: C1 ).
> > Automatically increasing to ...
> > .....
> > .....
> > .....
> > Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (
> > ID:0, Name: C1 ).
> > Automatically increasing to 1107290000.
> > Segmentation fault ( core dumped).
> >
> >
> > I have Ambertools18, Pr.Case.
> >
> >
> > With Regards.
> >
> >
> >
> > Le lun. 19 nov. 2018 à 23:27, David Case <david.case.rutgers.edu> a
> écrit :
> >
> >> On Mon, Nov 19, 2018, soukaina louerdi wrote:
> >>
> >>> I have AmberTools18.
> >> Also, if you put something like "fullerene gaff" in your subject line,
> >> you might be responses from people that have looked at similar
> >> compounds. Just saying "PCBM" might not trigger the right response.
> >>
> >> Also, be sure to do a Google seardh on "fullerene gaff": it looks like
> >> there are some interesting hits there.
> >>
> >> (Actually, even searching on "PCBM gaff" gets some hits....)
> >>
> >> ....dac
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Maura Malinska
> Assistant Professor
> Faculty of Chemistry
> University of Warsaw
> ul. Ludwika Pasteura 1, 02-093 Warsaw, Poland
>
> tel. 22 55 26 356
> mmalinska.chem.uw.edu.pl
>
> www.uw.edu.pl,
> http://crystal.chem.uw.edu.pl/staff/malinska.html
>
>
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Received on Fri Nov 23 2018 - 14:30:02 PST
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