Re: [AMBER] catenan simulation problems

From: Cristina Sisu <>
Date: Fri, 6 Mar 2009 15:28:00 +0000

Hi David,

I created the pdb file using $AMBERHOME/exe/ambpdb -p cat.prmtop <
cat.inpcrd > cat.pdb .
In antechmber I used similar commands as the ones presented in the
antechamber tutorial, but the list is:

$AMBERHOME/exe/antechamber -i cat1.pdb -fi pdb -o cat1.mol2 -fo mol2 -
c bcc -s 2

$AMBERHOME/exe/parmchk -i cat1.mol2 -f mol2 -o cat1.frcmod

And in leap , i've used leaprc.ff99SB:

source leaprc.gaff
x = loadmol2 cat1.mol2
loadamberparams cat11.frcmod
solvateoct x TIP3PBOX 12.0
saveamberparm x cat_wat.prmtop cat_wat.inpcrd

When I view the solvated structure in pymol it looks fine, so I did
not think it was a problem.

I also must tell you that I've created the initial pdb structure with
hyperchem, and then in pymol I renamed the atoms in order to make them
compatible with antechamber.
I'll attach here the .mol2 and .frcmod files and the intial .pdb (from
hyperchem-pymol) and solvated molecule .pdb files.


On 6 Mar 2009, at 14:59, 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.
> ...thanks...dac
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Received on Sun Mar 08 2009 - 01:09:08 PST
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