Hello, I have got following error during MMPBSA.py calculation for PBSA MD simulation.
How to fix it?
********************************************************************
Beginning GB calculations with /home/mijiddorj/installs/amber14/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
mmpbsa_py_energy: malloc.c:2372: sysmalloc: Assertion `(old_top == (((mbinptr) (((char *) &((av)->bins[((1) - 1) * 2])) - __builtin_offsetof (struct malloc_chunk, fd)))) && old_size == 0) || ((unsigned long) (old_size) >= (unsigned long)((((__builtin_offsetof (struct malloc_chunk, fd_nextsize))+((2 *(sizeof(size_t))) - 1)) & ~((2 *(sizeof(size_t))) - 1))) && ((old_top)->size & 0x1) && ((unsigned long) old_end & pagemask) == 0)' failed.
File "/home/mijiddorj/installs/amber14/bin/MMPBSA.py", line 96, in
app.run_mmpbsa()
File "/home/mijiddorj/installs/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/mijiddorj/installs/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/mijiddorj/installs/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
self.prmtop))
CalcError: /home/mijiddorj/installs/amber14/bin/mmpbsa_py_energy failed with prmtop ../achol.prmtop!
Exiting. All files have been retained.
******************************************************
I don't know anything about AMBER, but since you are getting a malloc error I can think of 4 things:
1) You are missing your C compilers when AMBER was being installed. How to install these varies on your operating system. If I knew your operating system I could be more helpful with this. If you have all of your dependencies installed, then this is clearly not the issue though.
2) You are running python 3.0 or higher instead of python 2.7 and this has created some sort of issue when communicating with the C extensions. I don't find this very likely, but the AMBER developers do say they do not support Python 3.0 or higher.
3) This is a memory issue. Your input is too large and allocating too much memory. Because of the python wrapper you are only getting very cryptic error messages and it is difficult to tell. All you can do is make sure your data is formatted correctly, and make sure the developer supplied example files run correctly.
4) This error is due to a bug in the code and you should contact the developers. Pinning down the source of memory allocation errors can be very difficult, but I'm sure the developers would be more than happy to resolve any issues.
I hope this helps. In short, make sure everything you need in addition to amber (e.g. C compilers) are installed. I ran across this site that might be helpful- http://jswails.wikidot.com/installing-amber14-and-ambertools14. Aside from making sure your input is formatted correctly (i.e. no unaccepted characters), you will have to contact the developers.
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