<br><div>This is exactly what I thought.</div><div>I found out that saving the file with .mol ending in PyMol does not give the unwanted bonds.</div><div><br></div><div>Thank you all.</div><div><br class="webkit-block-placeholder">
</div><div><br><br><div class="gmail_quote">On Thu, Nov 12, 2009 at 8:49 AM, Ran Friedman <span dir="ltr"><<a href="mailto:r.friedman@bioc.uzh.ch">r.friedman@bioc.uzh.ch</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
With VMD it's even simpler: use "dynamic bonds".<br>
<font color="#888888"><br>
Ran.<br>
</font><div><div></div><div class="h5"><br>
Nicolas Sapay wrote:<br>
><br>
><br>
> Dallas B. Warren a écrit :<br>
>><br>
>> Coordinate files like pdb and gro aren’t used by GROMACS to provide<br>
>> any bonding information. That is what the topology files are for. So<br>
>> their “presence” in your pdb isn’t an issue.<br>
>><br>
>> Actually, what is probably happening is that PyMol is guessing the<br>
>> bonds presence, based on the distance between atoms, and displaying<br>
>> it (which is what VMD does as well). So the bonds aren’t actually<br>
>> there at all in the pdb file.<br>
>><br>
> VMD can read/write CHARMM/NAMD topology files (namely psf files). If<br>
> your problem is *just* a visualization artefact, you can load your<br>
> structure in VMD, write a psf file and delete the unwanted bonds (this<br>
> does not require a specific forcefield). You can also combine 2 psf<br>
> files (1 for your protein and 1 for your ligand), that require some<br>
> basic knowledge of TCL though. After that, you just have to load the<br>
> topology abd the coordinates:<br>
><br>
> vmd -psf topology.psf -pdb coordinate.pdb<br>
><br>
> You won't see any weird bonds.<br>
><br>
> Nicolas<br>
>><br>
>> Catch ya,<br>
>><br>
>> Dr. Dallas Warren<br>
>> Drug Delivery, Disposition and Dynamics<br>
>> Monash Institute of Pharmaceutical Sciences, Monash University<br>
>> 381 Royal Parade, Parkville VIC 3010<br>
>> <a href="mailto:dallas.warren@pharm.monash.edu.au">dallas.warren@pharm.monash.edu.au</a><br>
>> +61 3 9903 9167<br>
>> ---------------------------------<br>
>> When the only tool you own is a hammer, every problem begins to<br>
>> resemble a nail.<br>
>><br>
>> *From:* <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a><br>
>> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>] *On Behalf Of *Gunnar<br>
>> Widtfeldt Reginsson<br>
>> *Sent:* Thursday, 12 November 2009 10:13 AM<br>
>> *To:* <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>> *Subject:* [gmx-users] Docking with PyMol and using Gromacs<br>
>><br>
>> Hi.<br>
>><br>
>> I am a new user of Gromacs.<br>
>><br>
>> My question is both PyMol and Gromacs related.<br>
>><br>
>> I tried the PyMol users mailing list but couldn't find anything.<br>
>><br>
>> I have a small organic molecule that I am inserting into DNA in pymol.<br>
>><br>
>> I have the DNA as one pdb file and the organic molecule as another<br>
>> pdb file. I open the DNA file in pymol and then load the organic<br>
>> molecule. After docking the organic molecule I write "save name.pdb"<br>
>><br>
>> When viewing the name.pdb file in pymol there are some bonds between<br>
>> the organic molecule and the DNA that I don't want. Somehow pymol<br>
>> creates them and I don't see those bonds in the name.pdb file when I<br>
>> open it in a text reader.<br>
>><br>
>> I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file<br>
>> of the organic molecule with topolbuilder 1.2 , and unite those .gro<br>
>> files and convert into a .pdb with editconf<br>
>><br>
>> The newly created pdb file still has those unwanted bonds.<br>
>><br>
>> My question is:<br>
>><br>
>> Can I ignore those bonds?<br>
>><br>
>> If not, how can I prevent pymol making those bonds?<br>
>><br>
>> Thanks.<br>
>><br>
<br>
</div></div><div><div></div><div class="h5">--<br>
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