I think you've only addresses half of what Ross mentioned. But, that might get us close enough.
The files he sent do not contain a TER card or any other indication (that I can see) to make it be two+ separate molecules. Instead, best I can tell, they create disulfide bonds within the same protein chain.
These behaviors might be related, of course. I agree they should be fixed.
:-) Lachele
Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA
lfoley.uga.edu
http://glycam.ccrc.uga.edu
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Monday, April 11, 2011 6:40 PM
To: AMBER Developers Mailing List
Subject: [AMBER-Developers] sleap bug repro
Hello everyone,
This email is meant to nail down the issue Ross reported with sleap a little
while ago. The bug is that if two separate *molecules* are combined with a
"bond" by hand in leap, sleap does NOT then consider them to be the same
molecule. Because of this, they can be imaged separately. If done so...
kaboom.
You can reproduce this with the following leap script:
source leaprc.ff99SB
l = sequence {ACE ALA NME}
k = sequence {ACE TYR NME}
translate k {0 0 10}
lk = combine {l k}
bond lk.2.CA lk.5.CA
solvateoct lk TIP3PBOX 10.0
saveamberparm lk stupid.parm7 stupid.rst7
quit
Running this with tleap, the relevant part of the prmtop file is:
%FLAG SOLVENT_POINTERS
%FORMAT(3I8)
6 1113 2
%FLAG ATOMS_PER_MOLECULE
%FORMAT(10I8)
55 3 3 3 3 3 3 3
3 3
Thus, the first molecule is ACE-ALA-NME-ACE-TYR-NME (55 atoms), which is
what we want. If run with sleap, we get
%FLAG SOLVENT_POINTERS
%FORMAT(3I8)
6 1081 3
%FLAG ATOMS_PER_MOLECULE
%FORMAT(10I8)
22 33 3 3 3 3 3 3
3 3
Here, ACE-ALA-NME and ACE-TYR-NME are separate molecules. (the 1113 vs.
1081 just shows that tleap packed a couple more water molecules inside... no
big deal). I think this is probably an issue that should be resolved prior
to the release of AT 1.5.
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Apr 11 2011 - 16:00:03 PDT
