Re: [AMBER-Developers] Re: [AMBER] ptraj, imaging for NAMD generated dcd files, Error in tokenize

From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
Date: Thu, 25 Feb 2010 13:41:43 +0000

On Thu, 25 Feb 2010 08:30:02 -0500
Daniel Roe <daniel.r.roe.gmail.com> wrote:

> Should be fixed now. For some reason in the transformImage command the
> keywords looked for were byre, bymo, and byat instead of byres,
> bymol, and byatom. I updated the keywords, should be fine and
> consistent with documentation now.

Don't forget about bymask.


> On Thu, Feb 25, 2010 at 8:14 AM, case <case.biomaps.rutgers.edu>
> wrote:
>
> > On Thu, Feb 25, 2010, Monika Sharma wrote:
> >
> > > Hey thanks.. It worked.. :) That was weird.. Now I have to look
> > > into code too. Thank you a lot..
> > >
> > > On Thu, Feb 25, 2010 at 6:25 PM, Hannes Loeffler <
> > Hannes.Loeffler.stfc.ac.uk
> > > > wrote:
> > >
> > > > On Thu, 25 Feb 2010 17:54:20 +0530
> > > > Monika Sharma <mondyn.gmail.com> wrote:
> > > >
> > > > > image origin center byres ":821,200-231" familiar com :2-173
> > > >
> > > > Try with 'byre' instead of 'byres'. (I know the manual says
> > > > otherwise but this is what the source code says.)
> >
> > This looks like a bug in the argumentStackContains() function,
> > which is in actions.c. Workaround for this particular case would
> > be to update lines 11199-11205; but the function doesn't seem to be
> > doing what its comments say it should(?).
> >
> > Anyone (Dan?) have time to take a look at this? Tom: you could
> > too, but I'd rather you put effort into updating the ptraj section
> > of the manual....
> >
> > ...thx...dac

_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Thu Feb 25 2010 - 06:00:05 PST
Custom Search