Dallas B. Warren a écrit :
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: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 -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 [email protected] +61 3 9903 9167 ---------------------------------When the only tool you own is a hammer, every problem begins to resemble a nail.*From:* [email protected] [mailto:[email protected]] *On Behalf Of *Gunnar Widtfeldt Reginsson*Sent:* Thursday, 12 November 2009 10:13 AM *To:* [email protected] *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 editconfThe 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.
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