[gmx-users] Docking with PyMol and using Gromacs

Ran Friedman r.friedman at bioc.uzh.ch
Thu Nov 12 09:49:22 CET 2009

With VMD it's even simpler: use "dynamic bonds".


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.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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