AMBER Archive (2006)

Subject: Re: AMBER: ERROR: The PDB file is not in the working directory

From: saurabh agrawal (imsam100_at_yahoo.co.in)
Date: Thu Dec 14 2006 - 05:38:05 CST

Hello,
I am sorry Francois, It is accepting PDB file on
cahnging file name to Mol.pdb. But still following
error is comming.

                    ---------------------------
                      * Welcome to R.E.D. II *
                         RESP ESP charge Derive
                                                      
                         
                       MOLECULE = Molecule
                       CHARGE = RESP
                      ---------------------------
                                                      
                         
                        * Selected QM Software *
                                GAMESS
                                                      
                         
                     * 1 Conformation(s) selected *
                                                      
                         
                               WARNING:
         No three atom based re-orientation found in
the PDB file
     Re-orientation will be done according to the
GAMESS Algorithm!
                                                      
                         
                               WARNING:
                 No connectivity information found in
the PDB file
            The Tripos Mol2 file(s) will NOT be
generated !
                                                      
                         
                         * Software checking *
           rungms
         [ OK ]
           gamess.00.x
         [ OK ]
           ddikick.x
         [ OK ]
           resp
         [ OK ]
 
   The structure/conformation(s) is/are being
optimized ... [ FAILED ]
        See the file "JOB1-gam1.log"
 
        Press Enter to exit

Is it bacause of using PCGAMESS?
saurabh

--- saurabh agrawal <imsam100_at_yahoo.co.in> wrote:

> Hello,
> Thanks for suggestion Francois, But it is not
> working
> Dear.
> Actualy I had generated the Electrostatic potentials
> with pcgamess, But i do not know, how to prepare
> input
> file for antechamber through GAMESS output. That is
> why i was trying RED so that it could become bit
> easy,
> But reverse is happening. If someone can tell me how
> to prepare Gamess output file to antechamber input,
> or
> how to debug the RED error, any one will be nice for
> me.
>
> Thanking in advance.
> saurabh
>
> --- FyD <fyd_at_u-picardie.fr> wrote:
>
> > Quoting saurabh agrawal <imsam100_at_yahoo.co.in>:
> >
> > > ---------------------------
> > > * Welcome to R.E.D. II
> *
> > > RESP ESP charge Derive
> > > MOLECULE = Molecule
> > > CHARGE = RESP
> > >
> ---------------------------
> > >
> > > * Selected QM Software *
> > > GAUSSIAN
> > >
> > > ERROR: The PDB file is not in the working
> > directory
> > > Press Enter to exit
> >
> >
> > Can you try this ?
> >
> > mkdir TEST
> > mv YourPDBfile Mol.pdb
> > cp RED-vII.pl TEST
> > cp Mol.pdb TEST
> > perl RED-vII.pl
> > or
> > perl RED-vII.pl > perl RED-vII.log
> >
> > Check that $MOL_START="./Mol.pdb" in R.E.D. II
> > (MAIN PROGRAM section, at the end of the code)
> >
> > It should work.
> >
> > regards, Francois
> >
> >
> >
>
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>
>
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