Hi Syed,
I don't quite understand what you are trying to say, but if you look into
the "mm_pbsa_readinput.pm" file at line 352, the program ends at that line
because it cannot understand/find prmtop for complex file. so, like I said
in the earlier email, please provide correct path (in the mm_pbsa.in) for
COMPT (complex prmtop) or you can put the complex prmtop in the same
directory as your mm_pbsa.in file.
Please read the instruction (in the amber manual) carefully. In fact, I
ponder for a while on the correct way of using this powerful program!
regards,
vanessa
On 1/26/07, Syed Tarique Moin <tarisyed.yahoo.com> wrote:
>
>
> --- vanessa wai <wai.vanessa.gmail.com> wrote:
> Hi,
>
> COMP is specified in the file mm_pbsa_readinput.pm or
> either in my input file i.e. mm_pbsa.in that i have
> copied both in my working directory or the same file
> found in
> /usr/local/amber8/src/mm_pbsa/mm_pbsa_readinput.pm as
> it is giving the following error.
>
> Died at
> /usr/local/amber8/src/mm_pbsa/mm_pbsa_readinput.pm
> line 352
>
> Thanks in advance
>
> > Syed,
> >
> > Hi.
> >
> > > COMPT must be specified (correctly)
> >
> > indicated that you need to put the correct path for
> > com's prmtop. You can
> > either put the full path like :
> >
> > COMPT
> > home/xxx/process/complex.prmtop
> >
> > or
> >
> > COMPT complex.prmtop
> >
> > where you put the prmtop in the same directory where
> > you have the input file
> > (like what Varsha suggested).
> >
> > Hope it helps.
> >
> > Regards,
> > Vanessa
> >
> > On 1/26/07, Varsha Goyal <vgusp.yahoo.ca> wrote:
> > >
> > > Hi,
> > > Easiest way to do is keep all prmtop files in same
> > > directory where you have mm_pbsa.in file.
> > >
> > > Thanks,
> > > Varsha
> > >
> > >
> > > --- Syed Tarique Moin <tarisyed.yahoo.com> wrote:
> > >
> > > > Hello,
> > > >
> > > > In the mm_pbsa.log, it has the following error.
> > if
> > > > wrong path of the input files or prmtop file,
> > how i
> > > > could put the path of these files.
> > > >
> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> > > >
> > > > Checking sanity
> > > > Checking GENERAL
> > > > COMPT must be specified (correctly)
> > > >
> > > >
> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> > > >
> > > > Thanks in advance
> > > >
> > > > --- vanessa wai <wai.vanessa.gmail.com> wrote:
> > > >
> > > > > Hi.
> > > > >
> > > > > Check with your mm_pbsa.log and probably you
> > can
> > > > > find the error there. my
> > > > > suspect will be wrong path for input files or
> > > > > parmtop files.
> > > > >
> > > > >
> > > > > Regards,
> > > > > Vanessa
> > > > >
> > > > > On 1/25/07, Syed Tarique Moin
> > <tarisyed.yahoo.com>
> > > > > wrote:
> > > > > >
> > > > > > Hello,
> > > > > >
> > > > > > I run the command
> > > > > >
> > > > > > " ./mm_pbsa.pl mm_pbsa.in > mm_pbsa.log &"
> > > > > >
> > > > > > but it is giving the following error.
> > > > > >
> > > > > > Died at
> > > > > >
> > > > >
> > > >
> > /usr/local/amber8//src/mm_pbsa/mm_pbsa_readinput.pm
> > > > > > line 352
> > > > > >
> > > > > > I want assistance
> > > > > >
> > > > > > Thanks in advance
> > > > > >
> > > > > > Syed Tarique Moin,
> > > > > > Junior Research Fellow,
> > > > > > H.E.J. Research Institute of Chemistry,
> > > > > > International Center for Chemical and
> > Biological
> > > > > Sciences,
> > > > > > University of Karachi, Karachi-75720,
> > Pakistan
> > > > > >
> > > > > > tarisyed.yahoo.com
> > > > > > tarisyed.hotmail.com
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> > >
> >
>
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> > > > Syed Tarique Moin,
> > > > Junior Research Fellow,
> > > > H.E.J. Research Institute of Chemistry,
> > > > International Center for Chemical and Biological
> > > > Sciences,
> > > > University of Karachi, Karachi-75720, Pakistan
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>
> Syed Tarique Moin,
> Junior Research Fellow,
> H.E.J. Research Institute of Chemistry,
> International Center for Chemical and Biological Sciences,
> University of Karachi, Karachi-75720, Pakistan
>
> tarisyed.yahoo.com
> tarisyed.hotmail.com
>
>
>
>
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Received on Sun Jan 28 2007 - 06:08:01 PST
