Hi,
I have already Ambertools13 installed. When I run mmpbsa.py I obtain
the same error as you reported
Error: Atom 12403 was assigned a lower molecule # than previous atom.
This can
Error: happen if 1) bond information is incorrect or missing, or 2)
if the
Error: atom numbering in molecules is not sequential. If topology did
not
Error: originally contain bond info, 1) can potentially be fixed by
Error: increasing the bondsearch cutoff offset (currently 0.200). 2)
can be
Error: fixed by either using the 'fixatomorder' command, or using
Error: the 'setMolecules' command in parmed.py.
Error: Could not determine molecule information for complex.top.
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for complex.top.
...
but the calculation does not abort and I can get the output file with
the energies. I don't understand the error “Atom 12403 was assigned a
lower molecule # than previous atom” because the _MMPBSA_complex.pdb and
the other files are correctly generated according to the masks and atom
12403 (the Mn atom) is correctly positioned in all the files for the
receptor, ligand and complex. Are these errors “real errors”?
I tried to fix the trajectory in cpptraj:
parm outoforder complex.top
trajin outoforder traj.mdcrd
fixatomorder outprefix reorder
trajout traj.mdcrd restart
but I didn't get any output. Could someaone please tell me how to use
the fixatomorder command to fix the whole trajectory and the
complex.top? Should I do the same for the top files of the ligand,
receptor and for the mutant files?
Thanks,
Alexandra
Em 2014-02-28 16:02, Jason Swails escreveu:
> On Fri, 2014-02-28 at 15:35 +0000, almarques wrote:
>> Hi,
>>
>> Thank you. Indeed I am using ambertools12 but ambertools13 will be
>> installed in the lab computers in the next few days. The error that
>> you
>> found is similar to the one reported in:
>>
>> http://archive.ambermd.org/201306/0453.html
>>
>> Since in my solvated topology file the Na+ ions are before the
>> non-standard water molecule bound to Mn atom do you think that I will
>> have to re-order the atoms (i.e, use fix_traj_parm.py)to assure
>> compatibility between the trajectory without water and ions and the
>> topology file of the complex without water and ions? Because, if I
>> extract a pdb from the trajectory without solvent/ions the atoms are
>> in
>> the same order as the pdb file generated from the topology file
>> without
>> water/ions.
>
> You should not use fix_traj_parm.py; it is incredibly slow [1] and
> fixatomorder in cpptraj will do it far more quickly. (Dan had not
> written fixatomorder when I wrote that script).
>
> While you might not _have_ to use fixatomorder for MMPBSA.py to work
> for
> your system, it will definitely not hurt. Once you have AmberTools 13
> installed and updated, I suggest fixing the trajectories using
> fixatomorder in cpptraj.
>
> HTH,
> Jason
>
> [1] I believe I made a critical performance mistake with
> fix_traj_parm.py in which coordinate access actually fetches
> individual
> coordinates out of the file rather than storing a whole frame in
> memory
> and accessing coordinates from there. I could probably make the
> script
> orders of magnitude faster by fixing that problem, but there's no
> point
> now that you can use fixatomorder in cpptraj.
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Received on Mon Mar 03 2014 - 03:30:02 PST
