I tried MMPBSA, with following input on amber tools 14 (AMBER12)
Sample input file with pb analysis
&general
startframe=15000, endframe=20000,interval=50,
verbose=2, keep_files=1,
/
&pb
istrng=0.1, indi=4, scale=2, inp=2,
/
when I included the option "ipb=1" in &general or &pb, it gives the same
error
InputError: Unknown variable ipb in &pb.
I also tried to include this option in input file generaed from " make
mdins". still I got same error.
I understand that "ipb" is given in the &cntrl name list while running
implicit simulations. what is the equivalent parameter while performing
MMPBSA calculations..
On Tue, Jun 23, 2015 at 9:46 PM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> You should be able to compare provided you get converged dG values from
> your simulations .. For this you might need quite long simulations.
>
> Vlad
>
> On June 23, 2015 6:04:31 PM CEST, Muthukumaran R <kumaran.bicpu.edu.in>
> wrote:
> >Thank you for the replies.
> >
> >I have started working on PBSA calculations.
> >
> >Even after running PBSA, is it meaningful to compare the binding
> >energies
> >of DNA and RNA with a common receptor (protein) ?
> >
> >
> >
> >On Tue, Jun 23, 2015 at 5:19 PM, Carlos Simmerling <
> >carlos.simmerling.gmail.com> wrote:
> >
> >> I agree with Vlad, I think that using PBSA for postprocessing makes
> >sense
> >> for systems like this. We recently developed a GB model for nucleic
> >acids,
> >> but this really is intended for MD where PB would be very slow. Since
> >speed
> >> isn't as important in your binding affinity calculation, you should
> >> probably use a more accurate model than GB, especially for nucleic
> >acids.
> >>
> >> On Tue, Jun 23, 2015 at 7:32 AM, Vlad Cojocaru <
> >> vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> >>
> >> > We had quite poor experiences with MMGBSA for protein-nucleic acids
> >> > interactions not only because we got completely unrealistic
> >absolute
> >> > binding free energies but also because of rather poor agreement
> >with
> >> > experiment of relative dGs. Therefore, we use MMPBSA.
> >> >
> >> > For the protocol we use see the paper by Merino et al. in Structure
> >2014
> >> > (Structural basis for the SOX dependent redistribution of OCT4 ...)
> >.
> >> > Although in the paper we focus mostly on DNA-mediated
> >protein-protein
> >> > interactions, we did play with the protocol to optimize as much as
> >> possible
> >> > the protein-DNA energies.
> >> >
> >> > A word of caution: multiple tests with the PBSA parameters beyond
> >those
> >> > specified via MMPBSA.py is required.
> >> >
> >> > We are also preparing a follow up study with more discussion on the
> >> > influence of the PBSA parameters on the results.
> >> >
> >> > Hope this helps
> >> > Vlad
> >> >
> >> >
> >> >
> >> > On June 23, 2015 12:32:15 PM CEST, Muthukumaran R
> ><kumaran.bicpu.edu.in>
> >> > wrote:
> >> > >Dear amber users,
> >> > >I found from literature and mailing list that implicit simulations
> >for
> >> > >nucleic acids is not properly parameterized. I have done explicit
> >> > >solvent
> >> > >simulations for protein-DNA and protein-RNA complexes. I want to
> >study
> >> > >the
> >> > >specificity of protien towards DNA/RNA, in this regard I have
> >performed
> >> > >binding energy calculations using mmgbsa (AMBER 12 and Amber tools
> >13)
> >> > >
> >> > >Input used:
> >> > > &general
> >> > > startframe=20000, endframe=25000,interval=50,
> >> > > verbose=2, keep_files=1,
> >> > > /
> >> > > &gb
> >> > > igb=5,
> >> > >
> >> > >Queries
> >> > >
> >> > >1. is it possible to study specificity using MM-GBSA.
> >> > >2. As it is a relative method, is it meaningful to compare the
> >binding
> >> > >energies of DNA and RNA?
> >> > >3. In regard to the gb model, I have adopted igb=5 (modified OBC
> >model)
> >> > >as
> >> > >used in "A Computational Study of Nucleosomal DNA Flexibility by
> >Jory
> >> > >Z.
> >> > >Ruscio and Alexey Onufriev". is this still an accepted model for
> >> > >studying
> >> > >nucleic acids.
> >> > >
> >> > >
> >> > >Apart from MM-GBSA, is there any other analysis/method for
> >studying the
> >> > >specificity of Protein towards DNA and RNA.??
> >> > >_______________________________________________
> >> > >AMBER mailing list
> >> > >AMBER.ambermd.org
> >> > >http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> > --
> >> > Sent from my Android device with K-9 Mail. Please excuse my
> >brevity.
> >> > _______________________________________________
> >> > 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
> >>
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Sent from my Android device with K-9 Mail. Please excuse my brevity.
> _______________________________________________
> 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
Received on Wed Jun 24 2015 - 01:30:03 PDT
