Dear Jason,
Thankyou for the reply, as you suggested I had modified the input file for MMPBSA calculations and added strip_mask, the file looks like this:
Input file for running PB and GB
&general
endframe=5000, verbose=1, keep_files=2, strip_mask=":WAT:SOD:CLA",
# entropy=1,
/
&gb
igb=2, saltcon=0.100
/
&pb
istrng=0.100
/
This time when I run the MMPBSA calculations using following script: $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
Their is some development in the GB calculations, but for PB calculations the same error appears as follows:
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...
5000 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...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB 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 416, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /home/cbme/amber14/bin/sander failed with prmtop complex.prmtop!
I read the mailing list and found the use of mdins for this calculations as I mentioned in my previous email, this error is concerns about the energy calculations some one suggested (
http://archive.ambermd.org/201303/0409.html), I tried this but I get the same error, as follows:
the script use:
to get mdins, used following script: $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
I got two files _MMPBSA_gb.mdins and _MMPBSA.pb.mdin, than I had made changes in the _MMPBSA_pb.mdin file and again, and file looks like this:
File generated by MMPBSA.py
&cntrl
nsnb=99999, dec_verbose=0, ipb=2,
ntb=0, cut=999.0, imin=5, igb=10, inp=2,
/
&pb
istrng=100.0, maxitn=1000,
fillratio=4.0, radiopt=0,
npbverb=1, accept=0.000001,
/
Running the script: $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
This time I got this output:
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...
5000 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...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with /home/cbme/amber14/bin/sander
calculating complex contribution...
calculating receptor 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 416, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /home/cbme/amber14/bin/sander failed with prmtop graphene.prmtop!
Exiting. All files have been retained.
The _MMPBSA_receptor_pb.mdout.0 gives following error in end:
1496 24.4165267723917
1497 24.4165267723917
1498 5.9391551608520
1499 5.6092020963603
1500 55.4321148346191
PB Bomb: pb_fdfrc: unknown ipb
What could be the reason this time, is it still with strip_mask or something else.? Could you please suggest me what could be done now ?
thanks in advance
Abhi
> 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 Sat Dec 13 2014 - 00:00:02 PST
