[gmx-users] weird problem about editconf and genbox

[Lin Xu]

Hi,
I have two questions concerning generating a solvent box for my protein using gromacs 3.3.1. 

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. 

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 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? 

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