[gmx-users] octanol water-partition coefficient

[Rajneet kaur Saini]

Dear users,
I want to find value of log P from the water-octanol partition coefficient of a small molecule. I am following Justin tutorial for free energy calculation in water system. i have two queries1. how to construct the system in which octanol is saturated with water in a cubic box?2. I am new  to programming. in first system where small molecule is placed in water, my job.sh file is not running.Following is the errorcorona2 at corona2-HP-Z820-Workstation:~/Documents/FEC$ /Home/Documents/FEC/em_steep_0.sh/
bash: /Home/Documents/FEC/em_steep_0.sh/: No such file or directory
corona2 at corona2-HP-Z820-Workstation:~/Documents/FEC$ /Home/Documents/FEC/job.sh/
bash: /Home/Documents/FEC/job.sh/: No such file or directory
corona2 at corona2-HP-Z820-Workstation:~/Documents/FEC$ /Home/Documents/FEC/job.sh
bash: /Home/Documents/FEC/job.sh: No such file or directory
corona2 at corona2-HP-Z820-Workstation:~/Documents/FEC$ ./job.sh
bash: ./job.sh: Permission denied
corona2 at corona2-HP-Z820-Workstation:~/Documents/FEC$ ./job.sh
bash: ./job.sh: Permission denied
corona2 at corona2-HP-Z820-Workstation:~/Documents/FEC$ ./job.sh
bash: ./job.sh: Permission denied

After failing this command I give single command for each step for energy minimization.
 gmx grompp -f em_steep_0.mdp -c coordinatefile.gro -p topol.top -o em_0.tpr


NOTE 1 [file em_steep_0.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 2210928293

-------------------------------------------------------
Program gmx, VERSION 5.0
Source code file: /home/corona2/Downloads/gromacs-5.0/src/gromacs/gmxpreprocess/topio.c, line: 727

Fatal error:
Syntax error - File topol.top, line 17
Last line read:
'[ moleculetype ]'
Invalid order for directive moleculetype
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------These are the first 17 lines of topol.top file.

;       
;       
;       This file was generated by PRODRG version AA100323.0717
;       PRODRG written/copyrighted by Daan van Aalten
;       and Alexander Schuettelkopf
;       
;       Questions/comments to dava at davapc1.bioch.dundee.ac.uk
;       
;       When using this software in a publication, cite:
;       A. W. Schuettelkopf and D. M. F. van Aalten (2004).
;       PRODRG - a tool for high-throughput crystallography
;       of protein-ligand complexes.
;       Acta Crystallogr. D60, 1355--1363.
;       
;       

[ moleculetype ]
; Name                       nrexcl
UNK                            3
How to solve this error?