Hi,
I have done a 5ns simulation for a protein-ligand complex and I want to
calculate the entropy of binding for this complex using Normal Mode
analysis.
I have restricted my calculation to include only the residues within 12
angstroms of the active site.
I run this nmode in serial in CPU mode of Tesla C2050 with a 16 GB RAM.
When i run this even for something as less as 2 frames, i get the following
error.
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
ptraj found! Using /usr/local/amber11/bin/ptraj
nmode program found! Using /usr/local/amber11/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...
500 frames were read in and processed by ptraj for use in calculation.
Beginning nmode calculations with mmpbsa_py_nabnmode...
Calculating normal modes for 2 frames
calculating complex contribution for frame 0
calculating receptor contribution for frame 0
calculating ligand contribution for frame 0
calculating complex contribution for frame 1
calculating receptor contribution for frame 1
calculating ligand contribution for frame 1
Traceback (most recent call last):
File "/usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py", line 1344,
in <m
odule>
outfile.write(str(nmodenorm))
File
"/usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py"
, line 2263, in __str__
totavg, totstdev = self.AvgStdev()
File
"/usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py"
, line 2302, in AvgStdev
stdev = self._tot_stdevs()
File
"/usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py"
, line 2319, in _tot_stdevs
sum += self.com_data[0][i] - self.rec_data[0][i] - self.lig_data[0][i]
IndexError: list index out of range
The input file that I used is as below:
Input file:
|--------------------------------------------------------------
|NMODE
|&general
| verbose=1, interval=5, strip_mdcrd=0,
|/
|&nmode
| maxcyc=50000, nminterval=250, nmode_igb=1,
|/
and the command I used to run this is "/usr/local/amber11/bin/MMPBSA -i
nm_5e.in -cp comp_strip.prmtop -rp prot_strip.prmtop -lp
ligand5e_vac.prmtop -y comp5e_md1_5_12a.mdcrd"
A file named "FINAL_RESULTS_MMPBSA.dat" is being generated but there is no
Delta S value in it.. The contents of this file is shown below:
| Run on Fri Jan 27 23:13:57 IST 2012
|Input file:
|--------------------------------------------------------------
|NMODE
|&general
| verbose=1, interval=5, strip_mdcrd=0,
|/
|&nmode
| maxcyc=50000, nminterval=250, nmode_igb=1,
|/
|--------------------------------------------------------------
|Complex topology file: comp_strip.prmtop
|Receptor topology file: prot_strip.prmtop
|Ligand topology file: ligand5e_vac.prmtop
|Initial mdcrd(s): comp5e_md1_5_12a.mdcrd
|
|Best guess for receptor mask: ":1-109"
|Best guess for ligand mask: ":110"
|Ligand residue name is "UNK"
|
|Calculations performed using 500 frames.
|NMODE calculations performed using 2 frames.
|
|All units are reported in kcal/mole.
|All entropy results have units kcal/mole (Temperature is 298.15 K).
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Can someone please tell me what is going wrong... Is the problem with the
memory available in the system?
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Received on Fri Jan 27 2012 - 23:00:02 PST
