I know this was discussed recently but I am having the same problem and I don't think the solution proposed is correct.
This is the previous thread:
http://archive.ambermd.org/201206/0014.html
The original problem is that running MMPBSA in amber12 using a solvated topology that fits the trajectory comes up with an error
TrajError: Solvated topology 0 has IFBOX == 0
Error occured on rank 0.
Exiting. All files have been retained.
Presumably this occurs because MMPBSA expects a topology file with box information and since the topology I had prepared was written with nobox, the error occurs at this stage.
Let me explain what I did and perhaps someone can suggest how to fix the problem.
I took a fully periodic trajectory of a complex between a protein and a ligand and processed it to retain the closest 100 waters to the ligands. I need this trajectory for another calculation.
Then I wrote the trajectory with the nobox option.
I then prepared a topology file that matches this trajectory, i.e. from a pdb file that contains the complex and 100 waters.
In amber11 this arrangement worked, but in amber 12 for some reason it checks the IFBOX and finds that it is 0, so it stops the run.
I hope I provided enough information. If not I can add whatever is needed to the explanation.
Thanks for your help.
Roman Osman
roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>
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Received on Fri Jul 13 2012 - 10:00:02 PDT
