Hi George,
Are you running with AmberTools 1.5? If not, I would suggest upgrading and
using a nab program specifically written for this (MMPBSA.py will use this
by default instead of sander, which will run faster than sander and give the
same results). Furthermore, I don't know if npbopt was implemented in
earlier versions (PBSA experts will have to comment here).
HTH,
Jason
On Thu, Aug 11, 2011 at 10:47 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Thank you Jason,
>
> I run
>
> 1. MMPBSA.py.MPI -O -i mmpbsa.in -make-mdins -o FINAL_RESULTS.dat -sp
> solvated_complex.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
> ligand.prmtop -y *.mdcrd
>
> This produces _MMPBSA_gb.mdin and _MMPBSA_pb.mdin. The latter is
>
> File generated by MMPBSA.py
> &cntrl
> ntb=0, cut=999.0, ntpr=1, imin=5,
> maxcyc=0, igb=10, ipb=1, inp=1,
> /
> &pb
> dbfopt=1, epsin=1, epsout=80, istrng=800.0,
> radiopt=0, sprob=1.4, space=0.5, maxitn=1000,
> cavity_surften=0.00542, cavity_offset=-1.008,
> fillratio=4,
> /
>
>
> 2. I edited the _MMPBSA_pb.mdin by adding npbopt=1 at the control name list
> and rerun MMPBSA.py as above using -use instead of make-mdins
>
> Although the program produced FINAL_RESULTS.dat it complained that "Cannot
> match namelist object name npbopt
> namelist read: misplaced = sign"
>
> 3. I repeated step 2 above but instead of adding npbopt=1 at the control
> name list, I added it in the &pb name list.
> I got "Error: No potential terms in sander output! Check output files."
>
> Your advice on which of the above steps is right will be most helpful
>
> Thanks
>
> George
>
> On Aug 11, 2011, at 3:30 PM, Jason Swails wrote:
>
> > Hi George,
> >
> > My mistake. -make-mdins and -use-mdins are command-line flags -- NOT
> > something that goes in the input file. I should have been clearer about
> > that.
> >
> > On Thu, Aug 11, 2011 at 7:17 AM, George Tzotzos <gtzotzos.me.com> wrote:
> >
> >> Jason,
> >>
> >> Many thanks for this. Let me see if I understand the process you
> describe.
> >>
> >> 1. I need to run MMPBSA.py with an input file such as:
> >>
> >> Input file for running PB and GB
> >> &general
> >> "-make-mdins",
> >> endframe=50, verbose=1,
> >> # entropy=1,
> >> /
> >> &gb
> >> igb=2, saltcon=0.100
> >> /
> >> &pb
> >> istrng=0.100,
> >> /
> >>
> >> Of course this doesn't work because -make-mdins is wrong. Can you please
> >> help with the syntax.
> >>
> >> 2. Assuming that all works, I should get a number of output files
> including
> >> _MMPBSA_pb.mdin. This I have to modify by including set npbopt=1.
> >>
> >
> > You should only see temporary input files created, that is
> _MMPBSA_gb.mdin
> > and _MMPBSA_pb.mdin (and maybe one or 2 others).
> >
> >
> >>
> >> 3. Re-run MMPBSA.py using the same input file as in step 1 with the
> >> modification that instead of -make-mdins, I use -use-mdins.
> >>
> >
> > On the command-line.
> >
> >
> >>
> >> 4. Repeat step 3 above with different saltcon values.
> >>
> >> Is this process what you suggested?
> >>
> >
> > If you want to compare different salt concentrations or ionic strengths.
> >
> >
> >>
> >> I also have a general questions. Forgive my ignorance as I am a novice.
> >> What is the difference between PBSA in AmberTools and MMPBSA.py?
> >>
> >
> > PBSA is the program written to actually solve the PB equation. MMPBSA.py
> is
> > more or less of a glorified bookkeeper and organizer. It arranges all of
> > the input files and data, sets up calculations, and calls different
> programs
> > (one of them being PBSA for solving the PB equation) to actually run the
> > calculation, then parses the output files at the end and calculates basic
> > statistics of the resulting data.
> >
> > HTH,
> > Jason
> >
> >
> >>
> >> Your help is greatly appreciated
> >>
> >> George
> >>
> >>
> >> On Aug 11, 2011, at 5:13 AM, Jason Swails wrote:
> >>
> >>> On Wed, Aug 10, 2011 at 7:10 PM, George Tzotzos <gtzotzos.me.com>
> wrote:
> >>>
> >>>> Jason,
> >>>>
> >>>> Thank you. Due to oversight I did not attach the script. I'm copying
> it
> >>>> below for easy reference. Is there something more that I should do
> under
> >>>> &pb? Can I use saltcon=x.xxx under &pb as well?
> >>>>
> >>>
> >>> istrng is PB's version of saltcon (ionic strength vs. salt
> >> concentration).
> >>> If you want to use the non-linear PB equation, you will need to run
> >> MMPBSA
> >>> with the -make-mdins flag, modify the _MMPBSA_pb.mdin file to use the
> >>> non-linear equation (set npbopt=1), then re-run MMPBSA with the
> >> -use-mdins
> >>> flag to make sure it reads in your modifications. Note that you need
> >> every
> >>> command-line flag present for each MMPBSA command (the first to create
> >> the
> >>> input files and the second to use the modified ones).
> >>>
> >>> HTH,
> >>> Jason
> >>>
> >>>
> >>>> Thanks in advance
> >>>>
> >>>> George
> >>>>
> >>>> Input file for running PB and GB
> >>>> &general
> >>>> endframe=50, verbose=1,
> >>>> # entropy=1,
> >>>> /
> >>>> &gb
> >>>> igb=2, saltcon=0.100
> >>>> /
> >>>> &pb
> >>>> istrng=0.100,
> >>>> /
> >>>>
> >>>> On Aug 10, 2011, at 11:04 PM, Jason Swails wrote:
> >>>>
> >>>>> If you really want to analyze salt effects, you should use the
> >> nonlinear
> >>>> PB
> >>>>> equation rather than GB, as it provides a better approximation.
> >>>>>
> >>>>> HTH,
> >>>>> Jason
> >>>>>
> >>>>> On Wed, Aug 10, 2011 at 9:26 AM, George Tzotzos <gtzotzos.me.com>
> >> wrote:
> >>>>>
> >>>>>> I'm trying to analyse the effect of ionic strength on the Delta G of
> >>>>>> binding of a protein-ligand complex.
> >>>>>>
> >>>>>> I've been trying to do this by changing saltcon in the script below
> >> from
> >>>>>> 0.1 through to 0.8. I've observed little or no difference which
> does
> >>>> not
> >>>>>> much experimental data.
> >>>>>>
> >>>>>> Is there something else I should be doing? Your advice will be much
> >>>>>> appreciated.
> >>>>>>
> >>>>>> Regards
> >>>>>>
> >>>>>> George
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
> >>>>>> AMBER.ambermd.org
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> Jason M. Swails
> >>>>> Quantum Theory Project,
> >>>>> University of Florida
> >>>>> Ph.D. Candidate
> >>>>> 352-392-4032
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> Jason M. Swails
> >>> Quantum Theory Project,
> >>> University of Florida
> >>> Ph.D. Candidate
> >>> 352-392-4032
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Aug 11 2011 - 08:30:03 PDT
