Hi,
First let me say that I highly recommend against working inside the exe
folder, there are many many reasons why that is bad practice.
What you should do is add a line in your .bashrc file to add the directory
to your path. Something like:
export PATH=$PATH:$AMBERHOME/exe/
If you do this, you can execute the ambertools executables from anywhere on
your system.
But your problem is not related to this practice.
It seems *you haven't built rism3d.snglpnt.*
You may want to reinstall Ambertools completely and make sure you build
rism3d.snglpnt. Read the installation output to make sure
this wasn't skipped for any reason.
Otherwise you can try to build rism.snglpnt in the source directory
yourself and copy it to the amber bin directory
(then link it to the exe directory). If you are inexperienced with linux
this may be too difficult.
The source code is in: $AMBERHOME/AmberTools/src/rism
-Dan
On Thu, Jan 5, 2012 at 1:19 PM, Sudarshan Debnath <
suarshandebnath.ku.rediffmail.com> wrote:
> Dear Sir,
>
> Thank you for your sending algorithm. Again I say that I am a user
> of AMBER11. I follow your tutorial and done it up to step4 (prepare
> solvent). I work in exe folder where the maximum program files (like
> sander, nab, rism1d etc) are present and the output files for my work are
> generated in the same folder.
>
>
>
> What I do as follows-
>
>
>
> tleap –s –f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
>
> >prot = loadpdb onesolute.pdb
>
> >saveamberparm prot 1L2Y_1.prmtop 1L2Y_1.inpcrd
>
> >savepdb prot 1L2Y_1.pdb
>
> >quit
>
>
>
> It produces three output files: 1L2Y_1.prmtop, 1L2Y_1.inpcrd and 1L2Y_1.pdb
>
>
>
> cat > SPC_NaCl.inp OUTLST='x', THEORY='DRISM', CLOSUR='KH',
>
> >NR=16384, DR=0.025, routup=384, toutup=0,
>
> ……….
>
> ………
>
> >&SPECIES
>
> >DENSITY=0.005d0,
>
> >MODEL="$AMBERHOME/dat/rism1d/model/Cl-.mdl"
>
> >/
>
> >EOF
>
>
>
> It produces one output file: SPC_NaCl.inp
>
> Then I used the following command-
>
>
>
> rism1d SPC_NaCl > SPC_NaCl.out
>
>
>
> It produces three output file: SPC_NaCl.out, SPC_NaCl.sav and SPC_NaCl.xvv
>
>
>
> Now I can’t understand what is the script file for 3D RISM? I simply use
> the following command-
>
>
>
> rism3d.snglpnt --pdb 1L2Y_1.pdb --prmtop 1L2Y_1.prmtop --closure kh --guv
> 1L2Y --xvv SPC_NaCl.xvv
>
>
>
> It shows that:
>
>
>
> bash: rism3d.snglpnt: command not found
>
>
>
> Then I use -
>
>
>
> ./rism3d.snglpnt --pdb 1L2Y_1.pdb --prmtop 1L2Y_1.prmtop --closure kh
> --guv 1L2Y --xvv SPC_NaCl.xvv
>
>
>
> It shows that:
>
>
>
> bash: ./rism3d.snglpnt: No such file or directory
>
>
>
> By the way in exe folder there is no executing file or folder having name
> rism3d or 3drism. I can’t guess what happens? Please let me know.
>
>
>
> Happy New Year. With the best regards,
>
> Sudarshan.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
--
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Received on Wed Jan 04 2012 - 21:00:02 PST
