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
