AMBER Archive (2007)

Subject: Re: AMBER: mm_pbsa error

From: vanessa wai (wai.vanessa_at_gmail.com)
Date: Thu Jan 25 2007 - 20:13:19 CST

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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> >
> >
> > 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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