[AMBER] Nmode error of MMPBSA.py

From: (wrong string) 陳昭同 <dond750507.gmail.com>
Date: Wed, 23 Mar 2011 17:30:36 +0800

Dear Amber users!

I use Amber11 to calculate entropy by Nmode of MMPBSA.py


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


   endframe=1, keep_files=2,




   nmendframe=1, drms=0.01,



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


    -0.28695E+04 -0.16768E+04 0.00000E+00 0.81106E+02


     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

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
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