AMBER Archive (2009)

Subject: Re: [AMBER] catenan simulation problems

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sat Mar 07 2009 - 17:25:07 CST

On Fri, Mar 06, 2009, Cristina Sisu wrote:
>>>
>>> I want to simulate a catenan. In the first instance I created a mol2
>>> file using antechamber. I submitted it to leap and managed to get the
>>> topology and coordinate files for both vacuum form and solvated
>>> molecule. However if I check the pdb file of the solvated molecule I
>>> notice that the molecule was split. The first ring is labelled
>>> correctly
>>> but the second ring is split in trio (like water) and the last 100
>>> water
>>> molecules are treated as one single molecule.

Thanks for sending the files. We had a report earlier about problems
with bad TER cards in the output of ambpdb:

  http://archive.ambermd.org/200512/0210.html

You might see if anything there seems to apply to your situation. I'll
take a look at your files when I have a chance (but others on the list
are encouraged to do so as well!)

...regards...dac

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