Yes my tgtrmsmask contains 953 atoms. Stated below is the way I have defined the mask:
tgtfitmask=":1-120.CA",
tgtrmsmask=":1-120&!.H="
The output says:
Mask ":1-120.CA" matches 120 atoms
Mask ":1-120&!.H=" matches 953 atoms
If you back calculate the number of atoms in the mask from Restraint energy they will be 931 and 947 respectively (they must be the same!!). I am using TGTMDFRC as 2.
Thanks for your input and suggestions.
With best regards,
Rahul Banerjee
________________________________________
From: Carlos Simmerling [carlos.simmerling.gmail.com]
Sent: Friday, April 08, 2011 2:06 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Restraint potential in Targeted MD
the code matches what you wrote. are you sure that is the correct #
atoms in the mask? check the sander output and see what is says for
each of your masks.
On Fri, Apr 8, 2011 at 1:56 PM, Rahul Banerjee
<rahul.banerjee.chemistry.msu.edu> wrote:
> Dear Amber users,
>
> I was doing TMD simulation for a small protein of 120 amino acids. The force constant (TGRMDFRC) I was using is 2. I was applying restrain force on all the heavy atoms (NTTGTRMS = 953) but aligning the structure with the reference structure based on their C* trace (120 C* atoms). I was trying to calculate the Restrain potential from the following equation in the Amber10 manual:
>
>
>
> E = 0.5 * TGTMDFRC * NATTGTRMS * (RMSD-TGTRMSD)**2
>
>
> If I calculate the restraint energy (RESTRAINT) for the given example and they come out to be slightly different (1.3761 and 2.0165 compared to 1.3443 and 2.0047 respectively). I have considered RMSD as "Current RMSD from reference" and TGTRMSD as "Current target RMSD" (please see the example below). Why there is such deviation? I guess it is not truncation error or something like that.
>
> Thank you for your input.
>
> With best regards,
> Rahul Banerjee
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> ===============================================================================
> NSTEP = 100 TIME(PS) = 0.200 TEMP(K) = 281.47 PRESS = 78.8
> Etot = -59693.3975 EKtot = 13225.6527 EPtot = -72919.0502
> BOND = 344.6748 ANGLE = 917.0819 DIHED = 1246.7549
> 1-4 NB = 437.6376 1-4 EEL = 6023.0834 VDWAALS = 9689.5997
> EELEC = -91579.2268 EHBOND = 0.0000 RESTRAINT = 1.3443
> EAMBER (non-restraint) = -72920.3945
> EKCMT = 5952.4662 VIRIAL = 5561.2691 VOLUME = 229880.0226
> Density = 1.0182
> Ewald error estimate: 0.7172E-04
> Current RMSD from reference: 0.788
> Current target RMSD: 0.750
> ------------------------------------------------------------------------------
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> ===============================================================================
> NSTEP = 150 TIME(PS) = 0.300 TEMP(K) = 294.87 PRESS = 118.7
> Etot = -58177.1508 EKtot = 13855.3267 EPtot = -72032.4775
> BOND = 367.8662 ANGLE = 962.7299 DIHED = 1283.7928
> 1-4 NB = 447.1210 1-4 EEL = 6022.8517 VDWAALS = 9476.6759
> EELEC = -90595.5197 EHBOND = 0.0000 RESTRAINT = 2.0047
> EAMBER (non-restraint) = -72034.4822
> EKCMT = 6235.2483 VIRIAL = 5646.1869 VOLUME = 229936.7782
> Density = 1.0179
> Ewald error estimate: 0.6539E-05
> Current RMSD from reference: 0.796
> Current target RMSD: 0.750
>
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>
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Received on Fri Apr 08 2011 - 12:00:05 PDT
