[gmx-users] my protein gets cut while preparing for em

[Guillem Plasencia]

Hello,

This is my first MD (besides the ones in GROMACS'  benchmark), i found the 
following problem while following John Kerrigan's tutorial for Drug-Enzyme 
complex (the first part, energy minimization), using my own protein and its 
crystallographic ligand i ran into the following:

-briefing:

i had repaired all gaps in the protein pdb i'm using by replacing the 
missing residues for the ones from another pdb of the same protein, and 
doing restricted energy minimization with Sybyl7.1 molecular modelling 
software. So the input for Gromacs had all gaps repaired in the protein 
part.

i also had the cristallographic ligand docked into the binding site (with 
very good fitting indeed).

-GROMACS part:

removed all waters, obtained a ligand topology with PRODRG2 server, and also 
a pdb2gmx protein topology (for the gmx force field, just one doubt: which 
force field would be better to do MD with docked drugs for which i need the 
PRODRG2 server? only gmx FF?). I merged both gro files (put the ligand into 
the protein's) renumbered atoms, added the #include "ligand.itp" in the 
protein's topology file and also the line telling to include 1 molecule of 
the ligand. Then made the box, and filled it with waters

editconf -bt dodecahedron -f file0.gro -o file.gro -c -d 1

genbox -cp file.gro -cs spc216.gro -o b4ion.gro -p file0.top

without apparently no other problem than the approx -1 overall charge, which 
i later neutralized adding 1 Na with genion as

genion -s b4ion.tpr -o b4em.gro -pname Na -np 1 -g genion.log

Then i was curious and did trjconv my system (before running mdrun energy 
minimization) into a pdb, and had a look at it, and i saw my protein was 
splitted in three different molecules, one was inside the water box (but far 
away from box center, lying in touch of one of the boxes' sides) and the 
other two parts were completely outside the box.  Worst of all, they were no 
more one single peptidic chain, but separated one.

Any hint about what's happening? Also, why do i see a cube water box if i 
chose a dodecahedron instead with editconf? Why my protein isn't centered, 
if i chose option -c? Why isn't it a single polypeptide instead of three 
single fragments?

Thank you very much !

Guillem.
Lead Molecular Design

P.D. I have all the files available, but didn't submit them because their 
length, but of course will do to ease tracing the problem.

--
Guillem Plasencia