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,
/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 28 2014 - 20:00:03 PDT
