[gmx-users] File 'urea.gro' does not exist or is not accessible.

[Justin Lemkul]

On 4/6/16 6:47 AM, Divya Dube wrote:
> Dear All,
> While using command for urea based simulation
> 'gmx insert-molecules -f protein_box.gro -ci urea.gro -nmol 6065 -o
> protein_sol.gro -p topol.top'
>
>
> Following error is prompted
>
> Error in user input:
> Invalid command-line options
>    In command-line option -ci
>      File 'urea.gro' does not exist or is not accessible.
>      Unknown command-line option -p
> --------------------------------------------
> Program:     gmx insert-molecules, VERSION 5.1.1
> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
> Function:    void gmx::CommandLineParser::parse(int*, char**)
>
> Error in user input:
> Invalid command-line options
>    In command-line option -ci
>      File 'urea.gro' does not exist or is not accessible.
>      Unknown command-line option -p
>
> Question: Where I can find this urea.gro file?
>

You'll have to create it.  The use of coordinate files as input requires that 
they actually exist.

-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

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