AMBER Archive (2007)

Subject: Re: AMBER: mm_pbsa error

From: vanessa wai (wai.vanessa_at_gmail.com)
Date: Sat Jan 27 2007 - 09:02:33 CST


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_at_yahoo.com> wrote:
>
>
> --- 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
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> > >
> >
>
> ____________________________________________________________________________________
> > > > > > Need Mail bonding?
> > > > > > Go to the Yahoo! Mail Q&A for great tips
> > from
> > > > > Yahoo! Answers users.
> > > > > >
> > > > >
> > > >
> > >
> >
> http://answers.yahoo.com/dir/?link=list&sid=396546091
> > > > > >
> > > > >
> > > >
> > >
> >
> -----------------------------------------------------------------------
> > > > > > The AMBER Mail Reflector
> > > > > > To post, send mail to amber_at_scripps.edu
> > > > > > To unsubscribe, send "unsubscribe amber" to
> > > > > majordomo_at_scripps.edu
> > > > > >
> > > > >
> > > >
> > > >
> > > > 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
> > > >
> > > >
> > > >
> > > >
> > >
> > >
> >
>
> ____________________________________________________________________________________
> > > > Don't get soaked. Take a quick peak at the
> > forecast
> > > > with the Yahoo! Search weather shortcut.
> > > >
> > http://tools.search.yahoo.com/shortcuts/#loc_weather
> > > >
> > >
> >
> -----------------------------------------------------------------------
> > > > The AMBER Mail Reflector
> > > > To post, send mail to amber_at_scripps.edu
> > > > To unsubscribe, send "unsubscribe amber" to
> > > > majordomo_at_scripps.edu
> > > >
> > >
> > >
> > > __________________________________________________
> > > Do You Yahoo!?
> > > Tired of spam? Yahoo! Mail has the best spam
> > protection around
> > > http://mail.yahoo.com
> > >
> >
> -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber_at_scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to
> > majordomo_at_scripps.edu
> > >
> >
>
>
> 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
>
>
>
>
> ____________________________________________________________________________________
> Get your own web address.
> Have a HUGE year through Yahoo! Small Business.
> http://smallbusiness.yahoo.com/domains/?p=BESTDEAL
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu