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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