Dr. Carlos,
thank you. I will try to use only PB with the mutagenesis and see what
happens. My system is a complex of two proteins and I am trying to study
protein-protein interactions using these tools. I first did the
calcualtions with igb=5 with radii=2 and now I am jsut trying to redo the
same calculations with igb=8 with radii=3. If I could run these
successfully wihtout errors I can compare the results between these two as
well. But these unexpected errors are what is causing all the trouble here.
I will wait for Dr. Jason or someone else to comment on the error message.
Thank you again,
Sincelrey,
Jag
Graduate student, Department of Chemistry,
Michigan State University, East Lansing, MI
On Mon, Apr 18, 2016 at 9:04 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> Jason or others may be able to help with the error, but I want to point out
> htat igb=8 is good for proteins as you say, but really for protein MD. Here
> you are doing protein-ligand binding, and igb=8 wasn't really trained for
> ligand binding calculations. Our GB is trained to try to reproduce PB
> calculations as well as it can given the approximate functional form. For
> postprocessing when you don't really need the speed and ability to quickly
> calculate forces, I suggest using PB directly.
>
> On Mon, Apr 18, 2016 at 8:50 AM, Jag Silwal <jagsilwal.gmail.com> wrote:
>
> > Dear Dr. Carlos and Dr. Jason,
> >
> > Thank you for your email.
> >
> > So, I recreated new prmtop using Xleap and I reran the alanine scanning
> for
> > 11 mutants, one at a time. I created new prmtop for wild type and
> basically
> > just copied the same for all mutations. But surprisingly seven of
> > my mutations gave me the following errors and didn't complete but rest of
> > them completed successfully. Now this is particularly weird for me
> because
> > when I used igb=5 before out of 11 mutations I tried, 9 ran successfully
> > and only two were giving the same kind of error message. I really don't
> > think it has anything to do with switching from igb=5 to igb=8 but it is
> > weird that I am getting this random error message saying that I have
> > problem with wildtype complex topology files even though it is running
> fine
> > with other mutations. I know it is hard to find the cause without
> analyzing
> > the topology files but I was wondering if you have any suggestions for
> this
> > at all?
> >
> > The following is the general script I used for each mutation. Do I have
> to
> > re-run GB and PB for wild type for each calculation? I think it is going
> to
> > be the same for wild type any way, no matter what mutations I try. right?
> > So, next I added "mutant_only=1" for those that didn't work before and it
> > worked fine....... Is it ok to do 'mutant_only=1" and just run the
> > calculations for mutants only. It looks like it worked that way for me
> for
> > some of the mutants? Can I then manually subtract the delta G of complex
> to
> > get Delta Delta G for the mutants??
> >
> > Any insights would be helpful!!
> >
> >
> > Thank you,
> > Sincerely,
> > Jag
> >
> > Script:
> >
> > &general
> >
> > startframe=500, endframe=3500, interval=5,
> >
> > verbose=2, keep_files=2, strip_mask=':WAT,CL',
> >
> > /
> >
> > &gb
> >
> > igb=8, saltcon=0.150,
> >
> > /
> >
> > &pb
> >
> > inp=1, radiopt=0, istrng=0.15, fillratio=4.0
> >
> > /
> >
> > &alanine_scanning
> >
> > /
> >
> >
> > ERROR:
> >
> > Loading and checking parameter files for compatibility...
> > mmpbsa_py_energy found! Using
> > /opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/mmpbsa_py_energy
> > cpptraj found! Using
> > /opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/cpptraj
> > Preparing trajectories for simulation...
> > Mutating trajectories...
> > 501 frames were processed by cpptraj for use in calculation.
> >
> > Running calculations on normal system...
> >
> > Beginning GB calculations with
> > /opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/mmpbsa_py_energy
> > calculating complex contribution...
> > calculating receptor contribution...
> > calculating ligand contribution...
> >
> > Beginning PB calculations with
> > /opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/mmpbsa_py_energy
> > calculating complex contribution...
> > Warning: inp=1 was old default
> > Warning: cavity_surften=0.0378 not recommended for inp=1, switching to
> > inp=1 default value: 0.0050
> > Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to
> > inp=1 default value: 0.000
> > Warning: sprob=.557 not recommended for inp=1, switching to inp=1 default
> > value: 1.400
> > File "/opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/MMPBSA.py",
> > line 104, in <module>
> > app.run_mmpbsa()
> > File
> >
> >
> "/opt/software/Amber/14Tools15--Intel-13.0.1.117/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> > line 218, in run_mmpbsa
> > self.calc_list.run(rank, self.stdout)
> > File
> >
> >
> "/opt/software/Amber/14Tools15--Intel-13.0.1.117/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> > line 82, in run
> > calc.run(rank, stdout=stdout, stderr=stderr)
> > File
> >
> >
> "/opt/software/Amber/14Tools15--Intel-13.0.1.117/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> > line 431, in run
> > self.prmtop) + '\n\t'.join(error_list) + '\n')
> > CalcError:
> > /opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/mmpbsa_py_energy
> failed
> > with prmtop complex.prmtop!
> >
> >
> >
> > On Sun, Apr 17, 2016 at 11:00 AM, Jason Swails <jason.swails.gmail.com>
> > wrote:
> >
> > > Carlos is correct in that you need to regenerate a prmtop file with the
> > > desired radii (and that it affects both GB and PB as long as radiopt=0
> in
> > > the PB simulations). However, you don't have to go through tleap to do
> > > this. ParmEd allows you to do this very easily and very quickly with
> the
> > > 'changeRadii' command. So a ParmEd script like the following will do
> > what
> > > you want:
> > >
> > > parmed.py -p <your_prmtop> -i input_file
> > >
> > > where input_file contains
> > >
> > > changeRadii mbondi3
> > > parmout new_radii.prmtop
> > >
> > > ---
> > >
> > > This will create a topology file "new_radii.prmtop" with the mbondi3
> > radii
> > > instead of whatever you had before. It recognizes the same keywords
> that
> > > tleap does.
> > >
> > > HTH,
> > > Jason
> > >
> > >
> > > On Sun, Apr 17, 2016 at 7:53 AM, Carlos Simmerling <
> > > carlos.simmerling.gmail.com> wrote:
> > >
> > > > Changing the radii affects both PB and GB. You will be ok if you
> change
> > > > them now and use the new prmtop for mmpbsa.
> > > > On Apr 16, 2016 11:20 PM, "Jag Silwal" <jagsilwal.gmail.com> wrote:
> > > >
> > > > > Dr. Carlos,
> > > > >
> > > > >
> > > > > Thank you for your prompt reply. With the little knowledge I have I
> > > > didn't
> > > > > know that the radii were not used for any of the calculations
> during
> > > MD.
> > > > As
> > > > > you have suggested, if I just recreate new files in Xleap with new
> > > radii
> > > > > and use those along with coordinate file from production step I
> would
> > > be
> > > > ok
> > > > > then, right? For e.g. I would like to use a script similar to the
> one
> > > in
> > > > > tutorial with command line:
> > > > >
> > > > > $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o
> FINAL_RESULTS_MMPBSA.dat
> > > -sp
> > > > > ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp ras.prmtop -lp
> > > raf.prmtop
> > > > -y
> > > > > *.mdcrd
> > > > >
> > > > >
> > > > > I just thought that the .mdcrd files from the production step is
> > > related
> > > > to
> > > > > the radii set during the Xleap step and that would matter if I
> wanted
> > > to
> > > > > change the radii later after the simulation. But obvious lyI was
> > wrong.
> > > > > Does changing the radii affect PBSA results or is it just the GB?
> > Just
> > > > > curious.
> > > > >
> > > > >
> > > > > I will just recreate initial top and crd files in XLeap and I will
> > > rerun
> > > > > GB and PB accordingly.
> > > > >
> > > > >
> > > > > Again thank you for your valuable time,
> > > > >
> > > > >
> > > > > Jag
> > > > >
> > > > >
> > > > >
> > > > > On Sat, Apr 16, 2016 at 11:33 PM, Carlos Simmerling <
> > > > > carlos.simmerling.gmail.com> wrote:
> > > > >
> > > > > > If your only use of gb is for post-processing, you can just
> > generate
> > > a
> > > > > new
> > > > > > prmtop with the radii you want and use that for post-processing.
> > You
> > > > > would
> > > > > > only consider rerunning if the radii were used during md. If you
> > did
> > > > > > standard md in explicit solvent the radii were not used so do not
> > > > matter
> > > > > > for the md part.
> > > > > > On Apr 16, 2016 10:30 PM, "Jag Silwal" <jagsilwal.gmail.com>
> > wrote:
> > > > > >
> > > > > > > Dear all,
> > > > > > >
> > > > > > > I used "PBRadii mbondi 2" while generating topology and
> > coordinate
> > > > > files
> > > > > > in
> > > > > > > X-leap. I need to run MMPB/GBSA analysis after simulations.
> Based
> > > on
> > > > > the
> > > > > > > amber manual igb =8 is the best for proteins but now I can't
> use
> > > > igb=8
> > > > > > for
> > > > > > > GBSA because manual says that we have to use igb=2 or 5 for
> > PBRadii
> > > > > > > mbondi=2 setup.
> > > > > > >
> > > > > > > I already ran MMPB/GBSA analysis with igb=5 but I was wondering
> > if:
> > > > > > >
> > > > > > > a) There is a way to simply change the PBRadii mbondi to 3
> > without
> > > > > having
> > > > > > > to rerun the whole simulation again?
> > > > > > >
> > > > > > > b) I already ran PB/GB and alanine mutagenesis calculation
> using
> > > > > igb=5. I
> > > > > > > am guessing I need to rerun the calculation once the PBRadii is
> > > > > changed.
> > > > > > > right?
> > > > > > >
> > > > > > > Any helpful suggestions would be appreciated,
> > > > > > >
> > > > > > > Jag,
> > > > > > > _______________________________________________
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> > >
> > >
> > > --
> > > Jason M. Swails
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Received on Mon Apr 18 2016 - 07:00:03 PDT
