This is exactly what I thought. I found out that saving the file with .mol ending in PyMol does not give the unwanted bonds.
Thank you all. On Thu, Nov 12, 2009 at 8:49 AM, Ran Friedman <r.fried...@bioc.uzh.ch>wrote: > With VMD it's even simpler: use "dynamic bonds". > > Ran. > > Nicolas Sapay wrote: > > > > > > Dallas B. Warren a écrit : > >> > >> Coordinate files like pdb and gro aren’t used by GROMACS to provide > >> any bonding information. That is what the topology files are for. So > >> their “presence” in your pdb isn’t an issue. > >> > >> Actually, what is probably happening is that PyMol is guessing the > >> bonds presence, based on the distance between atoms, and displaying > >> it (which is what VMD does as well). So the bonds aren’t actually > >> there at all in the pdb file. > >> > > VMD can read/write CHARMM/NAMD topology files (namely psf files). If > > your problem is *just* a visualization artefact, you can load your > > structure in VMD, write a psf file and delete the unwanted bonds (this > > does not require a specific forcefield). You can also combine 2 psf > > files (1 for your protein and 1 for your ligand), that require some > > basic knowledge of TCL though. After that, you just have to load the > > topology abd the coordinates: > > > > vmd -psf topology.psf -pdb coordinate.pdb > > > > You won't see any weird bonds. > > > > Nicolas > >> > >> Catch ya, > >> > >> Dr. Dallas Warren > >> Drug Delivery, Disposition and Dynamics > >> Monash Institute of Pharmaceutical Sciences, Monash University > >> 381 Royal Parade, Parkville VIC 3010 > >> dallas.war...@pharm.monash.edu.au > >> +61 3 9903 9167 > >> --------------------------------- > >> When the only tool you own is a hammer, every problem begins to > >> resemble a nail. > >> > >> *From:* gmx-users-boun...@gromacs.org > >> [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Gunnar > >> Widtfeldt Reginsson > >> *Sent:* Thursday, 12 November 2009 10:13 AM > >> *To:* gmx-users@gromacs.org > >> *Subject:* [gmx-users] Docking with PyMol and using Gromacs > >> > >> Hi. > >> > >> I am a new user of Gromacs. > >> > >> My question is both PyMol and Gromacs related. > >> > >> I tried the PyMol users mailing list but couldn't find anything. > >> > >> I have a small organic molecule that I am inserting into DNA in pymol. > >> > >> I have the DNA as one pdb file and the organic molecule as another > >> pdb file. I open the DNA file in pymol and then load the organic > >> molecule. After docking the organic molecule I write "save name.pdb" > >> > >> When viewing the name.pdb file in pymol there are some bonds between > >> the organic molecule and the DNA that I don't want. Somehow pymol > >> creates them and I don't see those bonds in the name.pdb file when I > >> open it in a text reader. > >> > >> I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file > >> of the organic molecule with topolbuilder 1.2 , and unite those .gro > >> files and convert into a .pdb with editconf > >> > >> The newly created pdb file still has those unwanted bonds. > >> > >> My question is: > >> > >> Can I ignore those bonds? > >> > >> If not, how can I prevent pymol making those bonds? > >> > >> Thanks. > >> > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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