> 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:
>
> mmpbsa.in
>
> - without idecomp:
>
>
>
>
>
>
> *&general verbose=1, entropy=0, use_sander=1, netcdf=1,
> receptor_mask=":1-377", ligand_mask=":378"/&gb igb=8, saltcon=0.0/*
> -with idecomp:
>
> *&general*
>
>
>
>
>
>
>
>
>
>
> * verbose=1, entropy=0, use_sander=1, netcdf=1, receptor_mask=":1-377",
> ligand_mask=":378"/&gb igb=8, saltcon=0.0/!&decompidecomp=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 <http://mmpbsa.in> -o
> FINAL_RESULTS_MMPBSA.dat -sp cf1_c2.top -cp com.top -rp prot.top -lp
> ztr.top -y ../../../remd/gator/300.4K/tleap/c2/*.nc*
>
>
> 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>
> app.run_mmpbsa() File "/home/lucia/amber14/bin/MMPBSA_mods/main.py", line
> 218, in run_mmpbsa 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
> self.prmtop))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
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Received on Wed Jan 14 2015 - 09:30:04 PST
