[gmx-users] grompp error, invalid line in .gro file

[Justin A. Lemkul]

Just thinking out loud, but maybe "Argon" is too long of a name for the
residues.  The longest I think I've seen is 4 characters (something like LYSH
or ARGN, for example).  Maybe the length of the name is throwing off the
formatting.  Why don't you try again with a residue name of something like AR
(in both the .top and .gro, of course) and see if that fixes things.

-Justin

Quoting Andreas Kring <akring at fys.ku.dk>:

> Hello all.
>
> I'm trying to simulate an argon liquid. The OPLS-AA force field is used
> with the files from /usr/local/gromacs/share/gromacs/top. But I get an
> error when I run
>
> $ grompp -f NVT.mdp -c Ar.gro -p Ar.top
> -------------------------------------------------------
> Program grompp, VERSION 3.3.3
> Source code file: confio.c, line: 709
>
> Fatal error:
> Invalid line in Ar.gro for atom 1:
> 1Argon Ar 1 0.0 0.0 0.0
> -------------------------------------------------------
>
> An ideas on what can be wrong? My argon .top file and .gro file can be
> seen below.
>
> Kind regards
> Andreas
>
> ----------------------
> Ar.top
> ----------------------
> ; Topology file for Ar
>
> ; Parameter level
>
> #include "ffoplsaa.itp"
> ;            #define _FF_OPLS
> ;            #define _FF_OPLSAA
> ;            [defaults]
> ;            #include "ffoplsaanb.itp"
> ;               [atomtypes]
> ;            #include "ffoplsaabon.itp"
> ;               [bondtypes]
> ;               [constrainttypes]
> ;               [angletypes]
> ;               [dihedraltypes]
>
> ; Molecule level
>
> [ moleculetype ]
> ; molname	nrexcl
> Argon		1
>
> [ atoms ]
> ; id	at_type	res_nr	res_name	at_name	cg_nr	charge
> 1	opls_097	1	Argon	Ar	1	0.0
>
> ; System level
>
> [ system ]
> Argon liquid
>
> [ molecules ]
> Argon 2048
>
> ---------------------------------
> Ar.gro
> ---------------------------------
> fcc lattice of argon atoms
> 2048
> 1Argon Ar 1 0.0 0.0 0.0
> 2Argon Ar 2 0.283835 0.283835 0.0
> ...
> 2047Argon Ar 2047 4.257525 3.97369 4.257525
> 2048Argon Ar 2048 3.97369 4.257525 4.257525
> 4.54136 4.54136 4.54136
>
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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