On Thu, 2014-12-11 at 03:05 +0000, Abhishek TYAGI wrote:
> Hi,
>
> I am able to convert my files to to amber format using CHAMBER and got
> the paramtop and inpcrd files. Now, I want to perform MMPBSA
> calculations my system firstmolecule-dna. The files I have is
> solvated, complex, receptor and ligand, and the Production.dcd file
> that I got from NAMD simulations. The files generated by MMPBSA of
> _MMPBSA_complex.pdb, _MMPBSA_repetor.pdb, _MMPBSA_ligand.pdb having
> change in box size, the ions with dna moved away from firstmolecule,
> but, when I had checked the trajectory in VMD the MD looks correct.
>
>
> I am using Ambertool 14 and Amber 14
>
> I had modified my files as instructed here
> (http://archive.ambermd.org/201303/0409.html) and my mdins files are
> as follows:
>
> $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o out.dat -sp
> solvated.prmtop -cp complex.prmtop -rp firstmolecule.prmtop -lp
> dna.prmtop -y ../Production.dcd -make-mdins
>
> _MMPBSA_gb.mdin
> File generated by MMPBSA.py
> &cntrl
> nsnb=99999, dec_verbose=0, ntb=0,
> surften=0.0072, extdiel=80.0, ncyc=0,
> cut=999.0, saltcon=0.1, imin=5, igb=2,
> /
>
> _MMPBSA_pb.mdin
> File generated by MMPBSA.py
> &cntrl
> nsnb=99999, ipb=2,
> ntb=0, cut=999.0, imin=5, igb=10,
> /
> &pb
> use_sav=0, sprob=1.4, dprob=1.4, inp=2,
> npbopt=1, eneopt=1, bcopt=5,
> npbverb=1, accept=0.000001,
> istrng=100.0, maxitn=1000,
> fillratio=4.0, radiopt=0,
> /
>
> I had modified the mmpbsa.in files too by adding use_sander=1 in &genral as follows:
This is unnecessary. MMPBSA.py will automatically use sander if chamber
topologies are encountered.
> Input file for running PB and GB
> &general
> endframe=10000, verbose=1, use_sander=1,
> # entropy=1,
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100,
> /
>
> Finally, I got this error again and again, the "_MMPBSA_complex_gb.mdout.0" file is attached.
>
> $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o out.dat -sp solvated.prmtop -cp complex.prmtop -rp firstmolecule.prmtop -lp dna.prmtop -y ../Production.dcd -use-mdins
>
> Loading and checking parameter files for compatibility...
> CHAMBER prmtops found. Forcing use of sander
> sander found! Using /home/cbme/amber14/bin/sander
> cpptraj found! Using /home/cbme/amber14/bin/cpptraj
> Preparing trajectories for simulation...
> 10000 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with /home/cbme/amber14/bin/sander
> calculating complex contribution...
> File "/home/cbme/amber14/bin/MMPBSA.py", line 96, in <module>
> app.run_mmpbsa()
> File "/home/cbme/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File "/home/cbme/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/home/cbme/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
> self.prmtop))
> CalcError: /home/cbme/amber14/bin/sander failed with prmtop complex.prmtop!
> Exiting. All files have been retained.
>
>
> I dont understand where is the problem?, can anyone help me to solve this problem ?
> What should I do to make it running??
The error in your output file says that there is a mismatch in the
number of atoms in your coordinate and topology files. This is often
caused when strip_mask does not strip the correct atoms from your
solvated topology file to match your complex.
For example: if strip_mask does *not* strip out ions but your complex
topology file still has ions, you will get this error. If you included
neutralizing counterions (which is incorrect) or structurally important
ions (which is OK) in your complex topology file but strip_mask caused
MMPBSA.py to strip out those atoms, you will get this error.
The default for strip_mask is given in the manual (and CHARMM uses
different ion names than Amber does). You may have to modify that in
order to get your calculation to work.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Dec 11 2014 - 06:00:02 PST
