[gmx-users] genbox output taking forever to complete

Justin A. Lemkul jalemkul at vt.edu
Sun Apr 17 03:17:32 CEST 2011

majid hasan wrote:
> Dear All,
> I am trying to add a single strand dna, and single walled carbon 
> nanotube in a box using the genbox command. After typing following command:
> genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2 2 
> -o cntdna.gro,
> I get: Reading solute configuration
> Containing 168 atoms in 1 residues
> Initialising van der waals distances...
> WARNING: masses and atomic (Van der Waals) radii will be determined
>          based on residue and atom names. These numbers can deviate
>          from the correct mass and radius of the atom type.
> Reading solvent configuration
> "Giving Russians Opium May Alter Current Situation"
> solvent configuration contains 648 atoms in 216 residues
> and then it takes forever to produce output.
> I tried to generate an output with just one molecule in solvent 
> (spc216.gro), and I ran into same problem. I suspect something is wrong 
> with my solvent input (file attached). I copied this file from 
> gromacs/tutor/water folder, though it looks reasonable when I view I 
> view the corresponding .pdb file in rasmol (I created .gro file from 
> .pdb file using editconf -f spc216.pdb -o spc216.gro).
> Could anyone please guide me about possible issues, and how to resolve 
> them?

You're asking genbox to do far too many things at once.  Divide your procedure 
into steps:

1. Set a box size using editconf for either the CNT or DNA.
2. Place DNA into box with CNT using genbox -ci -nmol 1 (or vice versa: CNT into 
DNA box, whichever order you want)
3. Solvate



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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