[gmx-users] solvent box outside protein

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Mar 30 22:17:25 CEST 2009

No, not this one again!

Why not search the archives? Or browse the wiki? Or follow a more
extensive tutorial on Gromacs:
http://nmr.chem.uu.nl/~tsjerk/course/molmod/ ?


2009/3/30 Halie Shah <haliepshah at gmail.com>:
> Hi,
> I just finished my energy minimization run on GROMACS 4.0.4 for my
> ligand/protein combination. I opened the minimized protein pdb and the
> original pdb in VMD to visualize, but saw that my minimized protein was
> outside the solvent box I had made. How should this be corrected? Below is
> what I specified for my commands:
> editconf -bt octahedron -f BR6.pdb -o BR6.pdb -c -d 0.7
> genbox -cp BR6.pdb -cs spc216.gro -o BR6_b4ion.pdb -p BR6.top
> Do I need to increase my -d value, and if so, to what? My protein is 244
> residues..not too big. Also, is spc216 the right water model I should use?
> Thanks much in advance,
> Halie Shah
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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