Thanks for reply
But what is here mean by converged?
Is it if I am running two different MD run with same parameter then rmsd of
these two should converged then only that trajectory used for MMPBSA
calculation?
Here I am using three trajectory method. So is here criteria of converged
trajectory also used for ligand as well as receptor along with complex
trajectory?
Here I am attaching a rmsd graph of wt complex can I call it converged trajectory?
> This just means that you have not run long enough MD trajectories,
> i.e. your free energy calculations have not converged ... if you do,
> the difference between different trajectories should be within the
> uncertainties of reported free energies.
>
> Ray
>
> On Mon, Jun 11, 2012 at 2:08 AM, Sangita Kachhap <sangita.imtech.res.in> wrote:
>>
>> Hello All
>> I have four protein-DNA complexes first is wt, second DNA mutant, third
>> protein
>> mutant and fourth both mutant. I have to calculate binding free energy of
>> these
>> complexes.
>>
>> When I ran MD simulation of all these and calculate binding free energy, I got
>> binding free energy as follows:
>> First MD
>>
>> wt = -77.4 kcal/mol
>> DNA mutant = -59.7 kcal/mol
>> protein mutant = -77.2 kcal/mol
>> both mutant = -73.9 kcal/mol
>>
>>
>> Second MD run
>>
>> wt = -72.9 kcal/mol
>> DNA mutant = -91 kcal/mol
>> protein mutant = -74 kcal/mol
>> both mutant = -86.8 kcal/mol
>>
>> Is it possible to reproduce the result? I also claulated residue wise energy
>> decomposition there also I am getting diffrent result residue which is not
>> involve in interaction energy of that residue in first MD run is unfavorable
>> (2.9 kcal/mol) but in second MD run become favorable (-10.7 kcal/mol). So I am
>> not able to justify my result.
>>
>> Is here my approach to claulate bindng free energy is correct, i.e. run two MD
>> simulation and then calculation of binding free energy is correct so that I
>> can
>> also calculate STD of two result or run MMPBSA two times of a single MD run
>> and
>> calculate STD of two MMPBSA calculation ?
>>
>> Can anybody please suggest me
>>
>>
>>
>> With regards
>>
>> Sangita Kachhap
>> SRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>> ______________________________________________________________________
>> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
>> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
>> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
>> पिन कोड/PIN CODE :160036
>> दूरभाष/EPABX :0172 6665 201-202
>>
>> _______________________________________________
>> 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
>
With regards
Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH
______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 11 2012 - 12:00:02 PDT
