Hi Dr. Jason,
All the same, I am very appreciated for your suggestion. Now, I am just doing other preparation. And once your new, software appeared, can you inform me? I want to use it at the first time. By the way, using the mmpbsa script, I did many mutational energy calculation work. In fact we have finished the manuscript, so I am just waiting for your new script and add the entropy part to my system. After all without entropy, it looks like lack something.
Best wishes,
Rilei Yu
--- 10年5月19日，周三, 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5月19日,周三,上午4:59
Hello Rilei,
The best I can say at this point is to look at the minimization and nmode
output files to see what the gradient is calculated as in each case, and/or
wait for a week until we release the new version of MMPBSA.py (which will be
a significant update including decomposition, nab-computed nmode, and a much
better parallel scheme that parallelizes all aspects of the calculation to
as many processors as you have frames, including nmode, through MPI
implemented in the python script itself).
All the best,
Jason
On Tue, May 18, 2010 at 9:10 AM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote:
> Very thanks for your response,
>
> Now, on the one hand i am waiting for your new program, on the other hand,
> I am trying to find out what is wrong with my system. Tonight, I monitored
> the entropy calculation process, and I am certain the minimization is
> converged. Unfortunately, the entropy of the receptor was still not
> calculated. What is more there is no bug or error was found at all.
> Tue May 18 22:53:09 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, mpi_cmd='mpirun -np 8', nproc=8,
> /
> &nmode
> nmstartframe=1, nmendframe=1,
> nminterval=1, maxcyc=50000,
> /
> 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)
>
> -------------------------------------------------------------------------------
>
>
> Rilei Yu
>
> --- 10年5月18日，周二, Bill Miller III <brmilleriii.gmail.com> 写道：
>
> 发件人: Bill Miller III <brmilleriii.gmail.com>
> 主题: Re: [AMBER] entropy-problem
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 日期: 2010年5月18日,周二,上午9:55
>
> What output files are made during the calculation? Are there any errors or
> warning messages in the minimization and/or nmode ouput files? It is
> difficult to pinpoint an explanation for your result without examining the
> output files. If you could attach those files it might help us troubleshoot
> your problem.
>
> -Bill
>
> On Mon, May 17, 2010 at 9:29 PM, Rilei Yu <yulaomao1983.yahoo.com.cn>
> wrote:
>
> > Dear Dr. Jason,
> >
> > I ever increased the number of minimization step to 20000, but it is
> still
> > failed to calculate the entropy of the receptor.
> > For the 3th time, I increase it to 30000, but everything is the same.
> > For the 4th time, I increase the drms to 0.002, it still does not work.
> >
> > It looks like, it will not work on my system to calculate the entropy!
> >
> > Can you give me more suggestions?
> >
> > Rilei Yu
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
> 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 Tue May 18 2010 - 19:00:04 PDT
