AMBER Archive (2007)

Subject: Re: AMBER: mm_pbsa error

From: Syed Tarique Moin (tarisyed_at_yahoo.com)
Date: Fri Jan 26 2007 - 00:04:22 CST

--- vanessa wai <wai.vanessa_at_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_at_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_at_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_at_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_at_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_at_yahoo.com
> > > > > tarisyed_at_hotmail.com
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > >
> > >
> >
> >
>
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> >
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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_at_yahoo.com
> > > tarisyed_at_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

tarisyed_at_yahoo.com
tarisyed_at_hotmail.com

 
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