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
Received on Tue Jun 23 2015 - 09:30:03 PDT
