Hello. Could this be because this topology has a zinc atom and aminoacid
side chains attacked to it. The parameters to all these atoms were
generated using the mtk++ procedure. I have also changed the LJ parameters
to the water molecule attached to the zinc atom, since the standard
parameters caused the hydrogen atoms to collapse. I ran parmed.py check
validity and I got a warning :
Determining validity of prmtop
/home/fabricio/amber12/bin/chemistry/amber/readparm.py:1046:
MoleculeWarning: Molecule atoms are not contiguous! I am attempting to fix
this, but it may take a while.
MoleculeWarning)
1 total warnings
NonUniversalWarning: Modified off-diagonal LJ parameters detected! Will
probably
not work with pmemd.cuda or mgdx!
Now I am worried. I have used pmemd.cuda to solvate and stabilize the
system. Everything seemed fine during the parameterization process. The
parameters I obtained are in accordance with similar parameters from ZAFF.
The structure seems all right. It maintains the expected tetrahedral
conformation etc. Am I to worry about some underlying problem here?
Thank you
Fabrício
2013/6/19 Jason Swails <jason.swails.gmail.com>
> On Wed, Jun 19, 2013 at 1:10 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Hi,
> >
> > On Wed, Jun 19, 2013 at 10:49 AM, Fabrício Bracht <fabracht1.gmail.com>
> > wrote:
> > > Hello. I am experiencing some issues with ambertools 13 while trying to
> > > analyse different systems. The first system is a "normal" pmemd.cuda
> > > simulation of a protein in water. When I type the command cpptraj -i
> > > rmsd.ptraj -p HOH_wat.prmtop, I get the following error:
> >
> > CPPTRAJ currently processes flags on the command line in order. This
> > means that what is happening is your input file (rmsd.ptraj) is being
> > read in before your topology file (HOH_wat.prmtop). However, since
> > some of your input depends on the topology file (namely the 'trajin'
> > command), it fails.
> >
> > > Error: Atom 5311 was assigned a lower molecule # than previous atom.
> > > Error: This can happen if bond information is incorrect or missing.
> > > Error: Detected # of molecules is 7615. If this is incorrect and your
> > > Error: topology does not have bond information (e.g. PDB file), try
> > > Error: increasing the bond search cutoff offset (currently 0.200000).
> > > Error: e.g. 'parm HOH_wat.prmtop bondsearch <new offset>'
> > > Error: This can also happen if the atoms in your molecules are not
> > > Error: sequential (e.g. molecule 1 is atoms 1-4,10-14 and molecule 2
> > > Error: is atoms 5-9,15-20). This can be fixed using the 'setMolecules'
> > > Error: command in parmed.py.
> > > Error: Could not open parm HOH_wat.prmtop
> >
> > As stated by the error message, this can be caused by either incorrect
> > bond information or if atoms are not sequential within your molecules
> > (I suspect the latter). Cpptraj requires that atoms in molecules be
> > sequential for speed (among other things). Did you try using the
> > 'setMolecules' command in parmed.py?
> >
>
> As a followup to this comment, this indicates an issue in which the
> topology file is broken. While the setMolecules command in ParmEd will fix
> the topology file, it does so by re-ordering the atoms inside so that each
> molecule is represented continuously in the prmtop.
>
> This invariably 'breaks' compatibility with the generated trajectory file
> since the atoms are now in a different order. This issue is currently
> caused in complex systems if you use the 'bond' command in tleap to link
> together different 'molecules'. The idea is to use setMolecules alongside
> a restart file right after the problematic topology is printed out with
> tleap so that it reorders both the restart file and the prmtop.
>
> Since this error is very frequently discovered in hindsight, I wrote a
> little Python script awhile ago that uses some of the new ParmEd
> functionality to reorder the prmtop and the trajectory at the same time.
> The link to the script is on my wiki:
> http://jswails.wikidot.com/helpful-scripts#toc21
>
> A couple caveats here:
>
> 1) This re-orders the prmtop and the trajectory simultaneously (use the
> --help argument to the script to find out how to use it)
>
> 2) This script requires an up-to-date AmberTools 13 installation, and
> AMBERHOME must be set. Therefore, the input trajectories and input prmtop
> must have the same atom ordering.
>
> 3) This script will _only_ read NetCDF files (ASCII trajectories would
> process WAY too slowly), and will only write out a NetCDF file. You can
> provide as many input trajectories as you want, but it will only print out
> one output trajectory.
>
> 4) This script requires Numpy as well as some version of the NetCDF
> bindings, so either install ScientificPython, py-netcdf, or the netCDF4
> python bindings.
>
> If you need to fix a trajectory, you can't use ParmEd to fix your prmtop.
> In the future, it may not be a bad idea to use the 'checkValidity' command
> in ParmEd for prmtops you create just to check that everything is OK (it
> will also catch common mistakes, like not setting disulfide bonds, that may
> save you lots of time and wasted simulation).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Wed Jun 19 2013 - 19:30:02 PDT
