hi, 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 > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
