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,
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > > _______________________________________________
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> > > > >
> > > > _______________________________________________
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> > > >
> > > _______________________________________________
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> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Apr 18 2016 - 06:30:04 PDT
