Lin Xu wrote:
Hi, I have two questions concerning generating a solvent box for my protein
using gromacs 3.3.1.
Any particular reason you're using software that is over four years old?
Gromacs 4.0.7 will give you a major speed upgrade, and lots of new features.
1) I used to use editconf to generate a dodecahedron box, then use genbox. It
used to work fine: $editconf -f protein.gro -o protein_box.gro -d 0.9 -bt
dodecahedron -c $genbox -cp protein_box.gro -cs spc216.gro -p example.top -o
protein_box_water.gro
But recently I found that using exactly the same command and input files, and
the same program installed, the protein is not centered in the box (I
download the structure and view it in pymol and vmd). I tried other box
types, for triclinic and cubic, it seems -c flag can be recognized, but not
for octahedron (nor dodecahedron). I wonder what things could be wrong.
Nothing is wrong. Most visualization software defaults to a triclinic
representation. If you want the dodecahedral unit cell properly displayed you
need to use trjconv -ur compact.
2) I have crystal structure for wild type protein, when I generated solvent
box for it, genbox didn't put waters in active site. Then I made two
single-point active site residue mutations using pymol: for a mutant
Thr->Ala, no water is put in active site neither, but for mutant Thr->Ser, a
water molecule is found in the active site. The presence of waters
drastically changed my simulation results. This is again different from what
I got in the past. I used to work with those three proteins and no waters
were added in their active sites. I assumed mutant Thr->Ser shouldn't have
water, since genbox delete extra waters according to VanderWaals radii, and
the three proteins (one real structure and two models built up by pymol) are
so highly similar. I wonder why the program decide to treat them differently,
this time?
I don't know exactly what's going on, but the behavior of genbox can be
influenced by the values of -seed and -vdwd. Otherwise, if water should or
should not be in the active site, sufficiently long restrained equilibration may
help.
I also tried using different box types and box dimensions for mutant
Thr->Ser, and found sometimes a water added, but sometime not. Is this
inconsistency normal?
Different box types and dimensions will influence the way genbox places cubes of
water in the active site. It's not an inconsistency if you're manipulating
other factors.
-Justin
Sorry for the long email. Those problems seem really weird to me. Any
guidance or hint would be highly appreciated. Thank you very much,
Lin Xu
Ph.D. Candidate Boxer lab, Chemistry Department Stanford University Stanford
CA 94305 (650)6448383
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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