Hi All
I have fixed both bugs, but I am having difficulties for "git pull" or "git push"
for "git pull" the error message was:
fatal: cannot pread pack file: No such file or directory
fatal: index-pack failed
for "git push" the error message was:
! [rejected] master -> master (non-fast forward)
error: failed to push some refs to 'gitosis.git.ambermd.org:/amber.git'
Maybe because the tree is locked for AT 1.5 release?
Anyway I attached the sources I revised here:
for 1) the origin is different in sleap to tleap.
the file I changed was :
amber/AmberTools/src/gleap/mortsrc/format/xyz.cpp
for 2) The iwrap issue when you manually bond two molecules together.
the file I changed was:
amber/AmberTools/gleap/mortsrc/ambfmt/energee.cpp
I also attached a test case for (iwrap.tar.gz) 2) as based on the example
from Jason.
I wonder if someone could try the new source to see if it really fixed the
problem?
Sincerely,
Wei
On Apr 11, 2011, at 6:56 PM, Ross Walker wrote:
> 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
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>>
>>
>> _______________________________________________
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>> AMBER-Developers.ambermd.org
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>
>
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- application/octet-stream attachment: xyz.cpp
Received on Mon Apr 11 2011 - 21:30:02 PDT
