[gmx-users] Docking with PyMol and using Gromacs

Nicolas Sapay nicolas.sapay at cermav.cnrs.fr
Thu Nov 12 09:39:39 CET 2009

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.

> Catch ya,
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at 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-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] *On Behalf Of *Gunnar Widtfeldt 
> Reginsson
> *Sent:* Thursday, 12 November 2009 10:13 AM
> *To:* gmx-users at 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.
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