I want to calculate the change in entropy due to binding of my polymer with
the cluster , here I am using nmode analysis.
Is there anyway I can specify my complex which consist of the two (these are
not bonded and I am running implicit solvent) of them during entropy
calculations .
I am calculating this change through the entropy after this polymer binds to
my cluster .
I am using Amber tools 1.5 .My input file
&general
startframe=1,endframe=10,keep_files=2,
/
&nmode
nmstartframe=1,nmendframe=10,
nminterval=5,nmode_igb=1,
/
MMPBSA -O -i nmode.in -o final_results.dat -cp complex.prmtop -y mdcrd
I get an error as
Found an invalid periodicity in the prmtop file: 0
Error:error during mmpbsa_py_nabnmode calculations!
Thanks
Kirtana
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Received on Fri Sep 23 2011 - 15:00:02 PDT
