Help with MMPBSA error message: b_fdfrc(): Atom out of focusing box******************

[Sally Heo]

Hello, 

I was running a MMPBSA.py analysis for one of my protein models and I am getting this error message:  b_fdfrc(): Atom out of focusing box****************** I am not sure what could be causing this error and would like some help please. 

I am not able to upload my output file with the error message because the file size is too big (0.99 GB). I tried to convert to a .dat file or compressing the file. 

[Sally Heo]

[marioe911116]

could you try to generate a small trajectory (5 frames for example) and send the files you are using?

[Sally Heo]

I am not able to send everything, but I have generated a small trajectory for 5 frames. 

[marioe911116]

without all the files I can't perform the proper tests. you can use this service to send the files around:

https://wetransfer.com/

[Sally Heo]

Thank you for this link. I was able to upload all my files. Here is the link to download all my files that were generated when I ran the trajectory for 5 frames. It will expire in 7 days. 

https://we.tl/t-LD5Op4W6We

[marioe911116]

I see you are using MMPBSA.py. This group is intended to provide support for gmx_MMPBSA which is a GROMACS program, not AMBER's. You can post the issue on one of AMBER's mailing lists.