[gmx-users] octanol water-partition coefficient

[Justin Lemkul]

On 9/2/16 5:08 AM, Rajneet kaur Saini wrote:
> 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
>

Here your environment variables are set up.  Note that /Home and /home are 
different.

> 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?
>
>

The parent topology is set up wrong.  But there's nothing diagnostic here to 
know what it actually is.  Note that raw PRODRG topologies are of poor quality 
and should not be used without significant refinement.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================