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.
best regards
Alexandra
Em 2014-02-27 17:37, Jason Swails escreveu:
> On Wed, 2014-02-26 at 22:13 +0000, almarques wrote:
>> Hi,
>>
>> Sorry for taking so long to reply but. I sent the files directly to
>> you
>> via dropbox.
>> The command that I used to run mmpbsa.py is:
>>
>> $AMBERHOME/bin/MMPBSA.py -O -i mm-pbsa.in -cp com_wt.top -rp
>> recCFH_wt.top -lp ligB_wt.top -y 2frames.mdcrd -mc 2Bmut_comp.top -ml
>> 2Bmut_lig.top -mr recCFH_wt.top&
>>
>>
>> And the mm-pbsa.in is
>>
>> sample input file for running alanine scanning
>> &general
>> startframe=1, endframe=2, interval=1,
>> verbose=1,
>> ligand_mask=':1-200,806,810',
>> receptor_mask=':201-805,807-809,811-813',
>> /
>> &pb
>> inp=1, radiopt=0, exdi=80, indi=3.0,
>> cavity_surften=0.00542, cavity_offset=-1.008,
>> fillratio=4, scale=2.0, linit=1000, istrng=0.100,
>> /
>> &alanine_scanning
>> /
>
> I cannot reproduce your error using AmberTools 13. I get a bunch of
> error/warnings along the lines of:
>
> 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 com_wt.top.
> Error: SetSolventInfo: No molecule information.
> Error: Could not determine solvent information for com_wt.top.
>
> This error has been described elsewhere, but for MMPBSA.py should not
> be
> an issue. Please make sure you are using the latest version of
> AmberTools 13 for this calculation.
>
> Good luck,
> Jason
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Received on Fri Feb 28 2014 - 08:00:02 PST
