[gmx-users] Docking with PyMol and using Gromacs

Dallas B. Warren Dallas.Warren at pharm.monash.edu.au
Thu Nov 12 00:25:58 CET 2009

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.


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
Sent: Thursday, 12 November 2009 10:13 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Docking with PyMol and using Gromacs



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?




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