I'm using xleap with graphical interphase so I've load pdb just from
graphical option Load pdb :)
May be it could be helpfull- when xleap or tleap loaded I obtained that
Welcome to LEaP!
(no leaprc in search path)
besides I've problem with variables of all amber programs.
before installation I've define path and set environment but after
installation in new terminal window I must to define path again.
Is there any way to define path for ambertools permamentary?
Thanks
James
2011/11/1 Pavan Giovanni <giovanni.pavan.supsi.ch>
> Hi,
> just to be sure I was clear...
> I suppose you load your pdb into leap using the command:
>
> $AMBERHOME/bin/tleap -f tleap.in
>
> where in your tleap.in file you have the command
>
> a=loadpdb x.pdb
>
> written inside, right?
> what happens to me quite often is that the file "tleap.in"
> itself become unreadable (and you receive "sintax error"
> messages)...not the .pdb file.
> so you could try to edit your tleap.in file in linux and
> just "add a space and remove the space and save"...after
> that it should work.
> if this is not useful for you, I am sorry but I don't
> think I can be useful in any manner... :-(
> just try
> bye
> giovanni
>
> On Tue, 1 Nov 2011 15:17:38 +0400
> James Starlight <jmsstarlight.gmail.com> wrote:
> > Pavan, hello!
> >
> > I've already tried to do that but it didnt work :(
> > I could not load any pdb's (even from example subdir
> >from amber tools)
> >
> > James
> >
> > 2011/11/1 Pavan Giovanni <giovanni.pavan.supsi.ch>
> >
> >> Dear James,
> >> this happened to me quite often...it could be a
> >>formatting
> >> error if you have modified the file in Windows and then
> >> you move it in linux via ssh or scp.
> >> just try to do that:
> >> edit the file in linux, make any modification (write a
> >> letter and delete it) and save again the file in linux.
> >> It should work.
> >> bye
> >> giovanni
> >>
> >> On Tue, 1 Nov 2011 03:44:07 -0700
> >> James Starlight <jmsstarlight.gmail.com> wrote:
> >> > Dear Amber Users!
> >> >
> >> > I have some problem with loading pdb files in the
> >>XLEAP
> >> >software.
> >> >
> >> > I've tried to load different pdb files but in any
> >>cases
> >> >I've obtained
> >> > ERROR: Syntax error
> >> >
> >> > What I've done wrong ?
> >> >
> >> > James
> >> > _______________________________________________
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> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
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> >>
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>
>
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Received on Tue Nov 01 2011 - 05:00:10 PDT
