it's best if you include the previous emails and replies so people can
follow the discussion.
I don't understand the output. You used a force constant of 0.005 (last
email) but the restraint energy is 1864 with a deviation of 6 A. Maybe
you've given us input and output from different runs?
In any case, a small force constant may not be enough to force your
structure to the target one. Even with a large force constant it might not
work, depending on the changes needed to get from initial and final. You'll
probably need to look at the structure visually, and try to understand why
it may not be able to reach the final structure. Is something blocking it?
targeted md is simple - it assumes that you can go downhill in rmsd and
reach the target structure. that is not always possible, but it very much
depends on what you're trying to model.
On Thu, Jan 27, 2022 at 2:27 AM Pranabesh Mandal (PhD, Bioinformatics
August-2019) <pranabesh.cusb.ac.in> wrote:
> Dear Carlos,
> The RMSD between the initial and final structure was15.374. The protein was
> moving towards the final pose.
> At the end step of the simulation result is
>
> NSTEP = 25000 TIME(PS) = 125.000 TEMP(K) = 300.07 PRESS =
> 18.6
> Etot = -1010255.9572 EKtot = 289179.9513 EPtot =
> -1299435.9085
> BOND = 14201.0200 ANGLE = 52898.5640 DIHED =
> 31543.0883
> 1-4 NB = 13358.7775 1-4 EEL = -143960.7010 VDWAALS =
> 136790.5034
> EELEC = -1407440.5066 EHBOND = 0.0000 RESTRAINT =
> 1864.7033
> EAMBER (non-restraint) = -1301300.6117
> EKCMT = 109285.4199 VIRIAL = 107397.5072 VOLUME =
> 4692401.4722
> SURFTEN =
> -50.4288
> CMAP = 1308.6427
> Density =
> 0.9845
> Ewald error estimate: 0.5038E-04
> Current RMSD from reference: 6.085
> Current target RMSD: 0.000
>
> ------------------------------------------------------------------------------
>
>
> A V E R A G E S O V E R 25000 S T E P S
>
>
> NSTEP = 25000 TIME(PS) = 125.000 TEMP(K) = 300.21 PRESS =
> 1.7
> Etot = -1008742.2826 EKtot = 289309.2538 EPtot =
> -1298051.5363
> BOND = 14165.1395 ANGLE = 52797.6975 DIHED =
> 31725.2004
> 1-4 NB = 13372.2128 1-4 EEL = -143935.4507 VDWAALS =
> 137548.7028
> EELEC = -1408624.2793 EHBOND = 0.0000 RESTRAINT =
> 3589.6065
> EAMBER (non-restraint) = -1301641.1428
> EKCMT = 109251.6375 VIRIAL = 109078.8946 VOLUME =
> 4695220.8457
> SURFTEN =
> 22.5679
> CMAP = 1309.6342
> Density =
> 0.9839
> Ewald error estimate: 0.2472E-04
> Current RMSD from reference: 6.085
> Current target RMSD: 0.000
>
> ------------------------------------------------------------------------------
>
>
> R M S F L U C T U A T I O N S
>
>
> NSTEP = 25000 TIME(PS) = 125.000 TEMP(K) = 0.57 PRESS =
> 36.7
> Etot = 3461.7944 EKtot = 548.2237 EPtot =
> 3112.5298
> BOND = 97.4918 ANGLE = 194.0957 DIHED =
> 162.4124
> 1-4 NB = 49.5120 1-4 EEL = 114.6908 VDWAALS =
> 527.6060
> EELEC = 1076.8994 EHBOND = 0.0000 RESTRAINT =
> 2154.4398
> EAMBER (non-restraint) = 958.0900
> EKCMT = 290.1392 VIRIAL = 3723.4229 VOLUME =
> 3241.7672
> SURFTEN =
> 105.5822
> CMAP = 24.9993
> Density =
> 0.0007
> Ewald error estimate: 0.1559E-04
> Current RMSD from reference: 6.085
> Current target RMSD: 0.000
>
> The force constant is small because of bad energy error with higher
> tgtmdfrc value(tgtmdfrc>2).
> I also tried with different tgtmdfrc between 1 to 0.005 and the lowest rmsd
> I ever observed is around 2. I also increased the nstlim but the initial
> confirmation never reached the final conformational state.
> Another reason for assigning a small tgtmdfrc was to minutely observe the
> conformational changes occuring in the structure.
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jan 27 2022 - 04:00:02 PST
