---------- Forwarded message ----------
From: Soumendranath Bhakat <bhakatsoumendranath.gmail.com>
Date: Fri, Apr 25, 2014 at 8:53 AM
Subject: Re: [AMBER] MMPBSA query
To: AMBER Mailing List <amber.ambermd.org>
Hi Arunima;
Just a quick answer. Always whenever you are starting a production run from
equil.rst please put irest=0 in the md.in file and you can run 4
independent MD production runs from that equil.rst point with different
initial velocities.
Say for example you run 5ns 4 times production run putting irest=0 from
equil.rst you will get 4 trajectories. Now in the input file put suppose
starting frame=1; end frame=5000; interval=5 that means you are processing
1000 frames for all 4 trajectories. Now you will get 4 different mmpbsa
outputs taking in account 4 different trajectories. The best way is to take
average of all of them. This practice is good in multiple MD simulation as
it removes statistical, solvatiojn, force field related errors.
For you example a mmpbsa.dat output from 5ns 4 times is shown below, where
T1, T2, T3 and T4 denotes four indeoendent trajectories starting from
different initial velocities.
*Complexes*
*ΔGbind*
*ΔEele*
*ΔEvdW*
*ΔGgas*
*ΔGsol*
*Wild*
T1
-46.5489±0.1251
-25.0332±0.1442
-48.3440±0.1012
-73.3772±0.1851
26.8283±0.1104
T2
-44.7706±0.1838
-24.2509±0.2109
-48.0673±0.1393
-72.3182±0.2853
27.5476±0.1630
T3
-44.7706±0.1838
-24.2509±0.2109
-48.0673±0.1393
-72.3182±0.2853
27.5476±0.1630
T4
-46.5489±0.1251
-25.0332±0.1442
-48.3440±0.1012
-73.3772±0.1851
26.8283±0.1104
*Tavg*
*-45.6597±0.1544*
*-24.6420±0.1775*
*-48.2095±0.1202*
*-72.8477±0.2352*
*26.4379±0.1367*
*Mutant*
*T1*
-38.2631±0.1157
-16.2502±0.2371
-42.1752±0.1006
-58.4254±0.2612
20.1624±0.2386
*T2*
-38.2631±0.1157
-16.2502±0.2371
-42.1752±0.1006
-58.4254±0.2612
20.1624±0.2386
*T3*
-38.2631±0.1157
-16.2502±0.2371
-42.1752±0.1006
-58.4254±0.2612
20.1624±0.2386
*T4*
-39.3164±0.1290
-19.2339±0.2360
-43.8000±0.1177
-63.0339±0.2549
23.7175±0.2088
*Tavg*
*-38.5251±0.1190*
*-16.9961±0.2368*
*-42.5814±0.1049*
*-59.5775±0.2569*
*21.0511±0.2311*
I believe if you calculate your mmgbsa with this approach you will get
statistically significant result with high experimental correlation.
On Fri, Apr 25, 2014 at 8:07 AM, Arunima Shilpi <writetoash28.gmail.com>wrote:
> Dear Sir
>
> Here in the command for MMPBSA/MMGBSA calculation following command has
> been used
>
> 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
> As per the tutorial instruction the production step was run 4 time for the
> analysis for 2ns.
>
> I have query as to whether we will consider the last step for production
> prod4.mdcrd for MMPBSA calculation or do we have to consider all the four
> steps of production (prod1.mdcrd,prod2.mdcrd,prod3.mdcrd, prod4.mdcrd)
>
> Here for protein-ligand interaction
>
> I used the following command for delta G calcultion by MMPBSA.
>
> MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> C1191I_DRG_solvated.prmtop
> -cp C1191I_DRG.prmtop -rp C1191I.prmtop -lp DRG.prmtop -y prod4.mdcrd
>
> Regards
> Arunima
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
--
Thanks & Regards;
Soumendranath Bhakat
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 25 2014 - 00:30:03 PDT
