Hi,
I recommend upgrading to AmberTools 15 - see if that helps first.
-Dan
On Tuesday, September 1, 2015, Sangeetha B <sangeetha.bicpu.edu.in> wrote:
> Dear Amber users,
>
> I want to calculate the binding free energy of a protein-protein complex.
> My complex contains metals which I have stripped before MMPBSA
> calculations.
> I used ante-MMPBSA to create the receptor and ligand prmtops from the
> complex prmtop. I also generated a stripped binpos trajectory with 101
> frames for MMPBSA.
>
> I used the stripped prmtop and stripped binpos to calculate RMSD using
> cpptraj to check the compatibility and it worked out fine. The cpptraj
> reads all 101 frames and calculates RMSD.
>
> I am using AmberTools 14 (update 3). I have previously performed MMPBSA for
> many protein complexes without any errors.
> My input file is:
>
> Sample input file
> &general
> verbose=2, keep_files=1,
> /
> &gb
> igb=5,
> /
>
> But for this complex I am getting the following error:
>
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using /opt/amber/amber14/bin/mmpbsa_py_energy
> cpptraj found! Using /opt/amber/amber14/bin/cpptraj
> Preparing trajectories for simulation...
> TrajError: start frame (1) > total frames (0)
> Exiting. All files have been retained.
>
> This error occurs for both serial and parallel runs.
>
> when the same complex is run in AmberTools 12, i get a "memory corruption"
> error.
>
> if i use "use_sander = 1", the complex alone runs fine and .mdout is
> created, but when shifting to receptor, the program fails with an error
> "invalid next read".
>
> I have tried several runs by creating new prmtops, using sander, with
> netcdf/mdcrd/binpos trajectories but the error persists.
> The temporary pdb and mdcrd files are generated properly but the MMPBSA
> calculations doesn't start due to the error.
>
> What may cause this error and how to solve this?
>
>
> Thank you,
>
> With regards,
> B. Sangeetha
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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Sep 01 2015 - 11:00:03 PDT
