Hi Lachele,
There are 'two' bugs here.
1) The origin is different in sleap to tleap.
This is not a bug per se but it makes the default output look weird in
vmd if one uses iwrap and does not reimage with ptraj. My vote is to fix
sleap to use the same box origin as tleap.
2) The iwrap issue when you manually bond two molecules together.
This is a REAL bug and needs to be fixed since otherwise using iwrap can
lead to explosions.
All the best
Ross
> -----Original Message-----
> From: B. Lachele Foley [mailto:lfoley.uga.edu]
> Sent: Monday, April 11, 2011 3:48 PM
> To: AMBER Developers Mailing List
> Subject: Re: [AMBER-Developers] sleap bug repro
>
> 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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>
>
>
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Received on Mon Apr 11 2011 - 17:00:03 PDT
