Hi Dac,
Thank you for the advice. I confirmed that the prmtop file does not contain a bond between the carbons with parmed.py (thankfully).
Cheers,
Parker
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: Monday, February 24, 2014 7:43 AM
To: AMBER Mailing List
Subject: Re: [AMBER] New bonds in PyMol?
On Mon, Feb 24, 2014, de Waal, Parker wrote:
>
> When visualizing my simulation in pymol I noticed that a new bond seems
> to form between two carbons in my ligand not present in the tleap output
> (paramaterized as cc and cd). Interestingly when I view the same pdb
> snapshot in UCSF Chimera or VMD the bond is not present.
Depending on what sort of input you give it, visualization programs can make
lots of different decisions about whether or not to show a bond between two
atoms. The default is often to use some pretty arbitrary distance criterion.
It's is generally not enough to say "I used pymol, or VMD...". What is shown
on the screen also depends on the type of file you use as input.
If you haven't yet done so, use the printBonds command in
http://scanmail.trustwave.com/?c=129&d=kL6L0x4Ao_79TfGWyE7sEf2Ye6LP9S9RIqVaCRuMmw&u=http%3a%2f%2fparmed%2epy to
determine which bonds are actually contained in the prmtop file. What is in
the prmtop file is what is really used by sander or pmemd.
...dac
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Received on Mon Feb 24 2014 - 05:30:04 PST
