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.
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Received on Wed Jan 04 2012 - 20:30:03 PST
