Hello,
This is occurring because your snapshots have not minimized within tolerable
limits (see the default drms value and default maxcyc). nmode will not
calculate the hessian for any snapshot that has a gradient higher than the
specified drms (which is what you're seeing here).
To fix this, increase maxcyc to a value that will be large enough to
minimize the structures to within tolerable limits.
Hope this helps,
Jason
P.S. On a related note, we will shortly be releasing a significant update to
the MM/PBSA python script (within a couple weeks, I'm hoping) that
calculates the entropy using a NAB program rather than nmode itself, which
should be a significant improvement over the current implementation.
On Sat, May 15, 2010 at 9:13 PM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote:
> Dear amber users,
>
> Last time, I ever asked the same problem: when I tried to calculate the
> entropy contribution to my system, I found it failed for the receptor part.
> Last time I used homology model, but this time, I changed to the crystal
> structure. However, this problem was still not solved. Can anyone give me
> more suggestions? Or can I send my system to you, in order to find the
> problem easier?
>
> Sun May 16 00:12:49 EST 2010
>
> Input file:
> --------------------------------------------------------------
> MMPBSA input file to run gb
> &general
> startframe=250, endframe=250, interval=1, verbose=0,
> ligand_mask=':411-427', receptor_mask=':1-205:206-410',
> initial_traj=0,
> /
> &nmode
> nmstartframe=1, nmendframe=1,
> nminterval=1,
> /
> end
>
> --------------------------------------------------------------
> Solvated complex topology file: complex_solvated.prmtop
> Complex topology file: complex.prmtop
> Receptor topology file: re.prmtop
> Ligand topology file: lig.prmtop
> Initial mdcrd: complex_md2.mdcrd
>
> Calculations performed using 1 frames.
> NMODE calculations performed using 1 frames.
>
> All units are reported in kcal/mole.
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
> ENTROPY RESULTS (HARMONIC APPROXIMATION) CALCULATED WITH NMODE:
>
> Complex:
> Entropy Term Average Std. Dev.
> -----------------------------------------------------------
> Translational: -1.0000 0.0000
> Rotational: -1.0000 0.0000
> Vibrational: -1.0000 0.0000
> Total: -1.0000 0.0000
>
>
> Receptor:
> Entropy Term Average Std. Dev.
> -----------------------------------------------------------
> Translational: -1.0000 0.0000
> Rotational: -1.0000 0.0000
> Vibrational: -1.0000 0.0000
> Total: -1.0000 0.0000
>
>
> Ligand:
> Entropy Term Average Std. Dev.
> -----------------------------------------------------------
> Translational: 14.4288 0.0000
> Rotational: 13.0056 0.0000
> Vibrational: 154.7418 0.0000
> Total: 182.1762 0.0000
>
>
> DELTA S total= -1.0000 +/- 0.0000
>
> NOTE: All entropy results have units kcal/mol. (Temperature has already
> been multiplied in as 300. K)
>
> -------------------------------------------------------------------------------
>
> Very thanks!
>
> Rilei Yu
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat May 15 2010 - 19:00:02 PDT
