AMBER Archive (2009)

Subject: Re: [AMBER] catenan simulation problems

From: Cristina S.D. Sisu (
Date: Fri Mar 06 2009 - 09:35:46 CST

Don't know if the attachments managed to get sent but here they are again.


On Mar 6 2009, David A. Case wrote:

>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. To be more specific it
>> looks like this:
>How did you create the pdb file? Can you list the exact commands you
>used in antechamber and leap, or provide the mol2 file? Maybe if we can
>reproduce the problem we can see what is going wrong.
>AMBER mailing list

  • application/octet-stream attachment: cat1.mol2

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