[gmx-users] genconf, grompp

[Justin A. Lemkul]

saly jackson wrote:
> Hi everybody
> 
> After using genconf to build a .gro file for example containing 100000 
> molecules, I want to use grompp to minimize the system as the following:
>   genconf -f H.gro -nbox 10 100 100 -o H-largebox.gro
> grompp -f minim.mdp -c H-largebox.gro -p topol.top -o HMin.tpr -maxwarn 1
> 

You should not invoke the -maxwarn option unless you completely understand the 
implications of the error(s) you are bypassing.

> Although I see in the H-largebox.gro file 100000 molecules coordination,
> I receive the following error after running grompp.
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.5.4
> Source code file: grompp.c, line: 1370
> 
> Fatal error:
> There was 1 error in input file(s)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> 
> "Just a Minute While I Reinvent Myself" (Red Hot Chili Peppers)
> 
> Would you please help me?
> 

There is no way to help you.  The actual error message is further up in the 
grompp output, which you have not included.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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