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
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