[AMBER] Solvation of a system in AMBER11.

From: Sudarshan Debnath <suarshandebnath.ku.rediffmail.com>
Date: 5 Jan 2012 04:19:37 -0000

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
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