[gmx-users] Re: invalid line

[Justin A. Lemkul]

sarah k wrote:
> dear Justin A. Lemkul,
> 
> thanks for your reply. You were right. Now, it works and generates the
> nitrogen box. But when I type:
> grompp_d -f ions.mdp -c 3INC_solv.gro -p topol.top -o ions.tpr
> 
> I recieve this error: source file: grompp.c, line: 362
> number of coordinates in coordinate file (3INC_solv.gro, 30560) does
> not match (topol.top, 44471)
> 
> Now what should I do?( there are 14753Sol file based on my vector number)

Not to repeat the error message too much, but whatever the contents of your 
coordinate file, they do not match the topology by a very large amount.  This is 
a common error, and the solution is discussed here:

http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

-Justin

> 
> Regards,
> Fatemeh Keshavarz

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

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

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