[gmx-users] Invalid line in coordinate file (grompp tool)

[Justin Lemkul]

On 10/2/13 8:21 AM, Andrew Bostick wrote:
> Dear users,
>
> I have used grompp command for minimising my system (protein and
> membrane). I am getting the error:
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.1
> Source code file: confio.c, line: 744
>
> Fatal error:
> Invalid line in system.gro for atom 11380:
>     6.98200   7.63300   7.36400
>
> For more information, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> First and end lines of my gro file are as follows:
>
> Giving Russians Opium May Alter Current Situation
> 11380
>     1DMPC    C1    1   4.752   4.493   5.267
>     1DMPC    C2    2   4.770   4.549   5.409
>      .
>      .
>      .
>      .
>      .
>   1834SOL     OW11378   2.802   5.473   1.849
>   1834SOL    HW111379   2.797   5.377   1.844
>   1834SOL    HW211380   2.812   5.501   1.758
>     6.98200   7.63300   7.36400
> ------------------------------------------------------
>
> Number in second line (11380) is equal to number of atoms in gro file
> (11380)?
>

It shouldn't be.  The second line in the .gro file specifies the number of 
atoms, which should always be (number of lines) - 3 (title, second line, box 
vectors at the end).

-Justin

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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