[AMBER] Problem with idecomp in MMPBSA

From: <lalvarez.qi.fcen.uba.ar>
Date: Thu, 15 Jan 2015 12:01:03 -0300 (ART)

    Dear all,
    I have run MMPBSA on a protein-ligand complex without problem but when
I tried to run the same adding the decomp term an error appeared and
the run was aborted.
    Here are the main files:


    - without idecomp:
      verbose=1, entropy=0, use_sander=1, netcdf=1,
      receptor_mask=":1-377", ligand_mask=":378"
      igb=8, saltcon=0.0
    -with idecomp:
      verbose=1, entropy=0, use_sander=1, netcdf=1,
      receptor_mask=":1-377", ligand_mask=":378"
      igb=8, saltcon=0.0
    idecomp=1, dec_verbose=0,
    print_res="205, 209, 236, 237, 238, 239, 317, 353, 354, 356, 363"

    The execution line:
    $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat
-sp cf1_c2.top -cp com.top -rp prot.top -lp ztr.top -y

    And finally, the error
    oading and checking parameter files for compatibility...
    Preparing trajectories for simulation...
    3100 frames were processed by cpptraj for use in calculation.

    Running calculations on normal system...

    Beginning GB calculations with /home/lucia/amber14/bin/sander
      calculating complex contribution...
     bad atom type: FE
      File "/home/lucia/amber14/bin/MMPBSA.py", line 96, in <module>
      File "/home/lucia/amber14/bin/MMPBSA_mods/main.py", line 218, in
        self.calc_list.run(rank, self.stdout)
      File "/home/lucia/amber14/bin/MMPBSA_mods/calculation.py", line 79,
in run
        calc.run(rank, stdout=stdout, stderr=stderr)
      File "/home/lucia/amber14/bin/MMPBSA_mods/calculation.py", line 148,
in run
    CalcError: /home/lucia/amber14/bin/sander failed with prmtop com.top!
    Exiting. All files have been retained.

I found in previous messages that it was neccesary to modified the mdread
file in sander adding these lines:
 else if (atype(1:1) == 'FE' .or. atype(1:1) == 'Fe') then
               x(l165-1+i) = 0.78d0 + 1.4d0
               x(l170-1+i) = 0.00000d0
               x(l175-1+i) = -0.00000d0
               x(l180-1+i) = -0.00000d0
               x(l185-1+i) = 0.00000d0
and reinstalling but I have already done this without success.

Any ideas of how overcome this problem?

Thanks, Lucía

AMBER mailing list
Received on Thu Jan 15 2015 - 07:30:02 PST
Custom Search