Hi,
We have since switched from using* nmode* to using a *nab* script to
calculate the entropy, which is a little more efficient . You are correct
that you can't use parameters such as nmode_igb=1 and nmode_istrng=0.1,
because these parameters were created for the *nab* entropy script. The
newest installation of MMPBSA.py can be found here at
http://ambermd.org/tutorials/advanced/tutorial3/py_script/compile.htm along
with an updated manual and instructions on how to install it. I would
strongly suggest switching to the updated version because the reason you
listed in your previous email is the reason for the development of the newer
nab script. In the nab script we checked to make sure the protein is
properly minimized and it will produce an error message if it is not so this
will better allow you to determine if it is an minimization error or a
memory problem.
On Wed, Mar 23, 2011 at 5:30 AM, 陳昭同 <dond750507.gmail.com> wrote:
> Dear Amber users!
>
> I use Amber11 to calculate entropy by Nmode of MMPBSA.py
>
> And
>
> 1. sorry my poor English
>
> 2. the article would quite long
>
>
>
> First,my Amber11 program is not update to lastest situation,and I have
> searched several similar question on Amber website.
>
>
>
> When I perform entropy calculation by using Nmode of MMPBSA.py,there are
> some problems still exist.
>
> Following is my input file
>
> Input file for running entropy calculations using NMode
>
> &general
>
> endframe=1, keep_files=2,
>
> initial_traj=1,
>
> /
>
> &nmode
>
> nmendframe=1, drms=0.01,
>
> maxcyc=20000,
>
> /
>
>
>
> So,I cannot use parameters such as “nmode_igb” or “nmode_istrng,and
>
> Endframe=1 is just I want to test quickly if it works.
>
>
>
> And it do not work properly,I check the _MMPBSA_complex_nm.out file
>
>
>
> ***************** ***************** *****************
>
> step = 0
>
> F = 0.374428E+02 GRDMAX = 0.151700E+01 GNORM = 0.234213E+00
>
> E-NONB E-ELE E-HBOND E-BOND
>
> -0.28695E+04 -0.16768E+04 0.00000E+00 0.81106E+02
>
> E-ANGLE E-DIHED E-NB14 E-EEL14
>
> 0.48807E+03 0.24746E+04 0.93756E+03 0.60244E+03
>
> E-POL E-3BOD
>
> 0.00000E+00 0.00000E+00
>
> Root-mean-square gradient of input coords is 0.234213414536555
>
> This is greater than the requested maximum: 0.100000000000000
>
>
>
> It means that structure energy doesn’t minimized to accepted value,so I
> change
>
> drms=0.03 of my input file,and it works.
>
> Then, I check _MMPBSA_complex_nm.out file again
>
>
>
>
>
>
>
> *******************************************************
>
> Initiate the NMODE module of AMBER 8
>
> *******************************************************
>
>
>
>
>
> File generated by MMPBSA.py
>
> ntrun maxcyc ibelly drms
>
> 1 100 0 0.30E+00
>
> rcut scnb scee dielc idiel
>
> 99.00000 2.00000 2.00000 4.00000 0
>
> nsave dfpred bdwnhl smx emx alpha ndiag
>
> 20 0.01000 0.10000 0.08000 0.30000 0.80000 10
>
> ipol = 0
>
> i3bod = 0
>
> idecomp = 0
>
> nvect = 0
>
> | New format PARM file being parsed.
>
> | Version = 1.000 Date = 02/14/11 Time = 11:47:12
>
>
>
> PARM file has the title:
>
>
>
>
>
> Total memory required : 274216136 real words
>
>
>
> Total memory required : 10430981 integer words
>
>
>
> Total memory required : 13797 4-character words
>
>
>
> Maximum nonbond pairs 10145259
>
>
>
> Duplicated 0 dihedrals
>
>
>
> Duplicated 0 dihedrals
>
>
>
> Getting coordinates from file with title:
>
>
>
> There were some questions I am frustrated
>
>
>
> 1. Did the output file shows Nmode module of Amber 8 is normally?
>
>
>
> 2. My goal is using drms=0.0001 of Nmode for entropy calculation,
>
> But no matter what “maxcyc” parameter number setting in the input file is
>
> (10000,20000,25000),there is always 100 of maxcyc in the complex_nm.out
> file
>
>
> And _MMPBSA_nmode_mincom.mdout.1 file really shows 20000 of maxcyc.
>
> Could someone tell me how to increase maxcyc to improve structure energy
> minimized in this situation?
>
>
>
> I believe it seems like energy minimized problem,rather than computer
> memory
>
> Is not enough.
>
> And I know the best way is update MMPBSA.py file correctly,but I just want
> to know that if it has some methods to achieve my goal.
>
>
>
> Attach file is my output file
>
> Thank you!
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Wed Mar 23 2011 - 06:30:04 PDT
