[gmx-users] Editconf error

[Justin Lemkul]

On 5/20/15 5:27 PM, Jorge Dagnino wrote:
> Dear GMX users.
>
> Im trying to create my system and When i use pdb2gmx everything seems ok.
>
> gmx pdb2gmx -f trim.pdb -o trim.gro -water spce -chainsep id
>
> Including chain 1 in system: 3235 atoms 203 residues
> Including chain 2 in system: 2531 atoms 161 residues
> Including chain 3 in system: 2546 atoms 161 residues
> Including chain 4 in system: 2531 atoms 161 residues
> Including chain 5 in system: 2546 atoms 161 residues
> Including chain 6 in system: 2842 atoms 169 residues
> Now there are 16231 atoms and 1016 residues
> Total mass in system 115288.734 a.m.u.
> Total charge in system -17.000 e
>
> Writing coordinate file...
>
> --------- PLEASE NOTE ------------
> You have successfully generated a topology from: trim.pdb.
> The OplsaaPBS force field and the spce water model are used.
>
> Then when i use the editconf command :
>
> gmx editconf -f trim.gro -bt dodecahedron -o box -c -d 1.0
>
>
> Read 16231 atoms
> Volume: 60.3503 nm^3, corresponds to roughly 27100 electrons
> No velocities found
>      system size : 11.777 11.005  6.369 (nm)
>      diameter    : 12.737               (nm)
>      center      :   -nan   -nan   -nan (nm)
>      box vectors :  4.144  4.582  3.178 (nm)
>      box angles  :  90.00  90.00  90.00 (degrees)
>      box volume  :  60.35               (nm^3)
>      shift       :   -nan   -nan   -nan (nm)
> new center      :   -nan   -nan   -nan (nm)
> new box vectors : 14.737 14.737 14.737 (nm)
> new box angles  :  60.00  60.00  90.00 (degrees)
> new box volume  :2262.99               (nm^3)
>
> and the ouptut file looks like this.
>
> Giant Rising Ordinary Mutants for A Clerical Setup
> 16231
>     27MET      N    1    -nan    -nan    -nan
>     27MET     H1    2    -nan    -nan    -nan
>     27MET     H2    3    -nan    -nan    -nan
>     27MET     H3    4    -nan    -nan    -nan
>     27MET     CA    5    -nan    -nan    -nan
>
> I try to make a bigger box manually, also change the box shape and the
> distance but i have the same result,
> This is my first time with this kind of error, what is wrong? what am i
> missing?

Hard to say; I've never seen anything like this.  The 'nan' means "not a number" 
so the coordinates are junk.  Are the coordinates in trim.pdb and trim.gro sound?

-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

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