[gmx-users] Docking with PyMol and using Gromacs

[Gunnar Widtfeldt Reginsson]

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.friedman at 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.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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