Hi Dr. Jason Swail,
Thanks for your reply! In fact, If did not make a mistake, I remember I had checked the out.put file. And I found the minimization stopped at about 4000 steps that is before 10000.
Because my system has five subunits, here I just used two subunits and the ligand to calculate the entropy. Was it this caused problem? Furthermore, can I calculate the entropy of part of the receptor. After it is extremely big! If I could, how set up?
Thanks for your reply again!
Rilei Yu
--- 10年4月15日，周四, Jason Swails <jason.swails.gmail.com> 写道：
发件人: Jason Swails <jason.swails.gmail.com>
主题: Re: [AMBER] Entropy-problem
收件人: "AMBER Mailing List" <amber.ambermd.org>
日期: 2010年4月15日,周四,上午6:31
Hello,
These results are obtained because no complex or receptor frame was
minimized within tolerable limits, so no nmode calculations were
actually done (except for the ligand). This is fixed in the version
that will be released on the web next in that it will not print a
table of -1's (which is what the average function returns as an error
for an empty set of values). I suggest you increase maxcyc in nmode
to something much much greater. You can get an idea of what it should
be by looking at the minimization mdout files that MMPBSA creates, and
estimating how many more steps would be needed to converge the
geometry to something tolerable.
Good luck!
Jason
On Wed, Apr 14, 2010 at 6:11 PM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote:
> Dear amber users,
>
> I spend very long time to finish the entropy calculation for a series of compex, what really makes me feel unexpected is the final values are completely the same (DELTA S total= -1.0000 +/- 0.0000). Can anyone give me some help? I am really appreciated!
>
> The following are two examples:
> Wed Apr 14 22:02:54 EST 2010
>
> Input file:
> --------------------------------------------------------------
> MMPBSA input file to run gb
> &general
> startframe=200, endframe=450, interval=50, verbose=0,
> ligand_mask=':421-432', receptor_mask=':1-210:211-420',
> initial_traj=0,
> &nmode
> nmstartframe=1, nmendframe=6,
> nminterval=1,
> /
> --------------------------------------------------------------
> 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 6 frames.
> NMODE calculations performed using 6 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: 14.2461 0.0000
> Rotational: 12.7523 0.0048
> Vibrational: 124.0036 1.2164
> Total: 151.0020 1.2147
>
>
> DELTA S total= -1.0000 +/- 0.0000
>
> NOTE: All entropy results have units kcal/mol. (Temperature has already been multiplied in as 300. K)
> -------------------------------------------------------------------------------
> -------------------------------------------------------------------------------
> Wed Apr 14 23:24:22 EST 2010
>
> Input file:
> --------------------------------------------------------------
> MMPBSA input file to run gb
> &general
> startframe=200, endframe=450, interval=50, verbose=0,
> ligand_mask=':421-432', receptor_mask=':1-210:211-420',
> initial_traj=0,
> &nmode
> nmstartframe=1, nmendframe=6,
> nminterval=1,
> /
> --------------------------------------------------------------
> 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 6 frames.
> NMODE calculations performed using 6 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: 14.1768 0.0000
> Rotational: 12.6221 0.0011
> Vibrational: 113.2362 0.4890
> Total: 140.0351 0.4903
>
>
> DELTA S total= -1.0000 +/- 0.0000
>
> NOTE: All entropy results have units kcal/mol. (Temperature has already been multiplied in as 300. K)
> -------------------------------------------------------------------------------
> -------------------------------------------------------------------------------
> 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 Wed Apr 14 2010 - 19:00:03 PDT
