Hi Gabriel,
You should continue this thread on the mailing list so it's archived and
people can benefit from them in the future.
On Wed, Apr 20, 2011 at 10:22 AM, Gabriel Urquiza <urquizagabes.gmail.com>wrote:
> Jason,
>
> I have done as you said and found out the topologies were kind of
> problematic. However, in tracking down the
> error I found out that leap is miswriting the topologies even though the
> files from which it writes are right. I can't
> find out what is going on. On the one hand, for instance, the ligand mol2
> is perfect. Then, after the topology has been
> written down, I check the results on VMD and it is hideous.
>
Be careful here if you're using ASCII trajectories. There are two options
for loading MDCRD files in VMD, and choosing the wrong one can give you this
effect.
Make sure that you're loading properly either "with periodic box" or not.
Note that if you run a solvated trajectory, you'll have to choose the one
"with box info". MMPBSA.py automatically strips the box information from
the trajectories, so in that case you DON'T want to load that kind of
trajectory.
An alternative to all of this is to just use netcdf trajectories (ioutfm=1
in your sander/pmemd input file), which VMD reads the same way whether or
not there is box information there.
>
> There is also one more puzzling event. When I use ambpdb to generate a PDB
> from the wrecked topolgies, the pdb comes
> out perfect, as if it had been written from good topologies. How can the
> very same pair topology-coordinates generate junk on
> vmd but also a perfect pdb? Is it common? Does the topology scheme has
> changed in Amber11? Perhaps VMD isn't showing
> data accurately? Is there any other visualizer for Amber11 topologies and
> coordnates?
>
I've never had problems with VMD/pmemd. My guess is that your topology is
not really "wrecked". Keep in mind that if you dump a PDB from the first
frame using a topology file and a trajectory file that has coordinates for
more atoms than you have in your prmtop file, your first frame will look
*fine*, since all of the atoms are present and in the correct place. After
the first frame, however, it will look awful, as the first atom of the
second frame will take the coordinates of the first atom after the last atom
present in the topology file (from the FIRST frame).
>
> I am more puzzled now than when I first started, but at least the
> checkCoordinates() problem was clarified =P. Do you have any clue
> on what's happening now? And by the way, is it even possible to run ten to
> twenty molecular dynamics trajectories with wrecked topologies?
> How come pmemd didn't crashed even before I generated the trajectories used
> in the mmgbsa calculations? Sorry to bomb you with all these
> doubts.
>
The only reason it wouldn't have crashed is because the topology file was
fine. If you used the topology file and coordinate file printed out by the
same Leap session, then your topology file is guaranteed* to be consistent
with your inpcrd file (*barring bugs, but at least the atom count between
them will match).
My guess is that you're having a problem with ions in your MM/PBSA
calculation. You adjusted the strip_mask so that it only gets rid of WAT
and Na+, yet are there other ions in your prmtop file? If there are, for
instance, Cl- ions in your solvated topology file that you took out when you
created your complex/receptor/ligand topology files, then you will run into
this problem. Alternatively, if you kept Na+ ions in your
complex/receptor/ligand topology files, then MMPBSA will have stripped them
out, your prmtops/trajectories won't match, and you'll also see this
problem.
HTH,
Jason
>
> Regards
>
> Gabriel
>
> 2011/4/20 Jason Swails <jason.swails.gmail.com>
>
>> On Tue, Apr 19, 2011 at 7:34 PM, Gabriel Urquiza <urquizagabes.gmail.com
>> >wrote:
>>
>> > Dear amberists,
>> >
>> > I am having some problemas when I try to run MMPBSA.py on several short
>> > dynamics. My system is an explicitly solvated protein with a
>> > ligand, sodium ions and a flavin residue (which has been parametrized
>> using
>> > antechamber and parmchk).
>> >
>> > I run it with this input:
>> >
>> > &general
>> > startframe=1,
>> > endframe=1000000,
>> > interval=50,
>> > verbose=2,
>> > keep_files=1,
>> > strip_mask=":WAT:Na+",
>> >
>>
>> You should leave this at its default value, unless you want to keep any
>> ions
>> in there.
>>
>>
>> > ligand_mask=":O01",
>> >
>>
>> If you don't specify both receptor_mask and ligand_mask, it will ignore
>> this
>> and just use the default.
>>
>> entropy=1,
>> > /
>> >
>> > &gb
>> > igb=5,
>> > saltcon=0.150,
>> > /
>> >
>> > &pb
>> > istrng=0.15, fillratio=4.0
>> > /
>> >
>> > The residue name is O01 because it is the first of a series of related
>> > compounds. I run MMPBSA.py and it gives me this:
>> >
>> > checkCoordinates(): Could not predict number of frames for AMBER
>> trajectory
>> > file: _MMPBSA_complex.mdcrd
>> > If this is not a compressed file then there is a problem
>> >
>>
>> This suggests that your prmtop files don't match the trajectory files that
>> are generated by MMPBSA.py.
>>
>>
>> > checkCoordinates(): Could not predict number of frames for AMBER
>> trajectory
>> > file: _MMPBSA_complex.mdcrd
>> > If this is not a compressed file then there is a problem
>> > checkCoordinates(): Could not predict number of frames for AMBER
>> trajectory
>> > file: _MMPBSA_complex.mdcrd
>> > If this is not a compressed file then there is a problem
>> > checkCoordinates(): Could not predict number of frames for AMBER
>> trajectory
>> > file: _MMPBSA_complex.mdcrd
>> > If this is not a compressed file then there is a problem
>> > Error: Sander output is missing values!
>> > VDWAALS = ************* EEL = -22412.2843 EGB =
>> > -3345.9563
>> >
>>
>> This all but confirms it. Try visualizing _MMPBSA_complex.mdcrd with your
>> complex prmtop, _MMPBSA_receptor.mdcrd with your receptor prmtop, and
>> _MMPBSA_ligand.mdcrd with your ligand prmtop. If the structures look
>> warped, then something is messed up and you have to fix your prmtops (or
>> just use the default strip_mask).
>>
>> HTH,
>> Jason
>>
>>
>> >
>> > ptraj found! Using /opt/amber11/exe/ptraj
>> > sander found! Using /opt/amber11/exe/sander (serial only!)
>> >
>> > Preparing trajectories with ptraj...
>> > Beginning quasi-harmonic entropy calculation with ptraj...
>> > 70 frames were read in and processed by ptraj for use in calculation.
>> >
>> > Starting sander calls
>> >
>> > Starting gb calculation...
>> >
>> > Starting pb calculation...
>> >
>> > NOTE: All files have been retained for debugging purposes. Type
>> MMPBSA.py
>> > --clean to erase these files.
>> >
>> > There are no values of GB or PB in the output. Something probably went
>> > wrong
>> > (no kidding?).
>> >
>> > I made PDB files for the minimization step and for several snapshots of
>> the
>> > dynamics using ambpdb. I also checked THE dynamics
>> > themselves. All of that using VMD. The snapshots seemed fine as well as
>> the
>> > trajectories. I also checked the topologies used by the
>> > MMPBSA.py and all of them were at the right place.
>> >
>> > I looked around the list for problems such as these but i didn't find
>> one
>> > that matched the context I am facing right now. Also, my trajectories
>> > aren't compressed.
>> >
>> > Looking forward to hear your ideas.
>> >
>> > Gabriel
>> >
>> > -----
>> > Graduation student at Federal University of Paraíba, Brazil.
>> > LQQC - Laboratory of Computational Quantum Chemistry
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Apr 20 2011 - 11:30:11 PDT
