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
Received on Tue May 18 2010 - 06:30:03 PDT
