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

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Mon Jun 19 19:49:06 CEST 2006


On Monday 19 June 2006 18:06, Guillem Plasencia wrote:
> 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?

tpbconv -c -pbc nojump should help, take as reference your starting structure 
which is complete in the box.

> 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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 Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de

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