Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna

From: Abhishek TYAGI <atyagiaa.connect.ust.hk>
Date: Mon, 15 Dec 2014 11:03:41 +0000

Hi, I had added strip_mask, that helped me to solve GB calculations, but when PB calculations started the new error pops out. The GB calculations are successful, but their is error in PB calculations and I am stuck to the error "PB Bomb: pb_fdfrc: unknown ipb" in my receptor output file _MMPBSA_receptor_pb.mdout.0 (attached). Please suggest me what to do to solve this problem. For your information, I had tried the following suggestions: http://archive.ambermd.org/201303/0550.html http://archive.ambermd.org/201303/0550.html http://archive.ambermd.org/201212/0028.html http://archive.ambermd.org/201110/0485.html my input file is as follows: 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 / Please suggest me some way to solve this error thanks in advance regards Abhi ________________________________________ From: Abhishek TYAGI Sent: Saturday, December 13, 2014 3:48 PM To: amber.ambermd.org Subject: Re: MMPBSA-ERROR for firstmolecule-dna 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 Mon Dec 15 2014 - 03:30:03 PST
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