[AMBER] Entropy calculation

From: asdda asa <nadaafiva.gmail.com>
Date: Wed, 29 Oct 2014 09:38:13 +0700

Dear Amber users,

I am performing entropy calculation using nmode.

My system consist of a protein with 213 residue and a ligand.

First, I did a try with only 4 frames and drms=0.1.

 My calculation succeed to reach convergence, but then fail with following
message:

 Line minimizer aborted: step at upper bound 0.061508653

Line minimizer aborted: step at upper bound 0.011450028

Line minimizer aborted: step at upper bound 0.025196144

Line minimizer aborted: step at upper bound 0.044987034

Line minimizer aborted: step at upper bound 0.00036005744

Line minimizer aborted: step at upper bound 0.003992881

FATAL: allocation failure in vector()

CalcError: /usr/local/AMBER/amber12/bin/mmpbsa_py_nabnmode failed with
prmtop complex.prmtop!

Exiting. All files have been retained.\


 From the massage, the problem might be due to prmtop file,

but I was using the same prmtop file to calculate entalphy, and it was
succesfull.


 I am using a single computer with 48 GB memory, so it should be no problem

with memory.

 Please your help.


Nadafiva

 Here is my Input file:

 &general

startframe=1, endframe=6000, keep_files=2,

/

&nmode

nmstartframe=1, nmendframe=2000,

nminterval=500, maxcyc=10000, drms=0.1,

/
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Received on Tue Oct 28 2014 - 20:00:03 PDT
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