I posted a question last week but no response, which leads me to conclude that perhaps I did not formulate it properly.
Here is my problem, perhaps someone can help.
I would like to calculate the energy of binding of a peptide to a protein using MMPBSA. I use two 100 ns trajectories of the protein-peptide complex and of the empty protein to create two new trajectories with 100 waters closest to the peptide binding groove of the peptide, respectively. I wrote them in ptraj with the nobox option. In the MMPBSA calculation I would like to use these trajectories but strip the waters from them. In addition, I have the trajectory of the peptide without water.
I created the appropriate topologies of the solvated complex and empty protein (each with the waters) as well as the topologies of the complex, protein and peptide without waters. Now I run the MMPBSA with the three trajectories and solvated and non-solvated topologies. The run stops with the following error:
.....
TrajError: Solvated topology 0 has IFBOX == 0
Error occured on rank 0.
Exiting. All files have been retained.
....
There are various messages in the file before and after, but it seems this is the critical error that causes the program to exit. If needed I can provide the entire file.
Trying to figure out what is the reason for this error it looks like MMPBSA expects a topology with a periodic box for the solvated topology, but my trajectory is actually after the extraction and has been written with nobox. The topology matches the trajectory as I can use it for other calculations.
The question is: Are there some expected rules about solvated trajectories and their corresponding topologies?
Perhaps someone can suggest how to go about it, other than the simple way of creating fully stripped trajectories.
Thanks for your help.
Roman Osman
roman.osman.mssm.edu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 16 2012 - 19:00:02 PDT
