Hello Everyone,
I did entropy calculation using two different protocols (described below)
and got different results.
*1.* Using the trajectory of 5ns with 250 frames I calculated the entropy
using standard *mmpbs_nmode.in* (pasted below),
nput file for running entropy calculations using NMode
&general
endframe=250, keep_files=2, strip_mdcrd = 1, strip_mask = ":WAT:Cl-",
entropy = 1,
/
&nmode
nmstartframe=1, nmendframe=250,
nminterval=50, nmode_igb=1, nmode_istrng=0.1,
/
and the *command* uesd: /opt/mpi/openmpi/1.3.3/intel/bin/mpirun -np $NSLOTS
/opt/apps/amber10/exe/MMPBSA.py.MPI -O -i mmpbsa_nmode.in -o
FINAL_RESULT_NMA_LI4.dat -sp pro_LI4.top -cp complex.top -rp protein.top -lp
ligand.top -use-mdins _MMPBSA_pb_append.mdin -y LI4_5ns.mdcrd </dev/null
Hence, *DELTA S total= -30.6164 +/- 3.9462*
*2.* Later I followed the tutorial (
http://www.teokem.lu.se/~ulf/Methods/mm_pbsa.html) and the section (new
method to calculate entropy), in order to lessen the time.
Here I selected all the residues(including water) within 8 A of ligand and
used its topology as -sp flag, protein and ligand within 8 A of range as -cp
flag, and only protein in 8 A range as -rp flag,
*mmpbs_nmode.in *file being same as above, and command used:
/opt/mpi/openmpi/1.3.3/intel/bin/mpirun -np $NSLOTS
/opt/apps/amber10/exe/MMPBSA.py.MPI -O -i mmpbsa_nmode.in -o
FINAL_RESULT_8A_NMA_LI4.dat -sp pro_with_watermodLI4_8A.top -cp
pro_modLI4_8A.top -rp pro_NoDRG_modLI4_8A.top -lp ligand.top -y
LI4_5ns.mdcrd </dev/null
but here, I got *DELTA S total= -18.2487 +/- 25.1860*
Anyone please help me with the reason for this and also, if I have followed
the correct protocol?
Thanks in Advance
--
--
SUNITA GUPTA
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Received on Fri May 13 2011 - 05:00:02 PDT
