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 doesnt 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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Received on Wed Mar 23 2011 - 03:00:03 PDT
