Dear Bill,
Thank you for responding. Well my system comprises of 190
residues with a total of 3112 atoms. I believe this is still a
relatively small system and I am performing the calculation in only 2
frames. So I am expecting this not to take so long (>10 hours of CPU
time).
Ok the long calculation time is one problem. The other problem is that
I am getting an Index error as mentioned below.
--------------------------------------------------------------
Traceback (most recent call last):
File
"/cluster/apps/x86_64/packages/amber11-patch-19/src/AmberTools/src/mmpbsa_py/MMPBSA.py", line 1344, in
<module>
outfile.write(str(nmodenorm))
File
"/cluster/apps/x86_64/packages/amber11-patch-19/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py", line 2263, in
__str__
totavg, totstdev = self.AvgStdev()
File
"/cluster/apps/x86_64/packages/amber11-patch-19/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py", line 2302, in
AvgStdev
stdev = self._tot_stdevs()
File
"/cluster/apps/x86_64/packages/amber11-patch-19/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
--------------------------------------------------------------------
I went through the mailing list to get an idea and people seem to have
this error message. Some have issues with defining the receptor or
ligand mask whereas other discussion is around Bugfix.
I think my issue is not with defining the mask as I can see from the
output file that the program has rightly guessed the receptor and
ligand mask.
-------------------------------------------------------------
|Input file:
|--------------------------------------------------------------
|sample input file for NMODE calculation
|&general
|startframe=1, endframe=10, interval=5,
|verbose=1, keep_files=0, strip_mdcrd=0,
|/
|&nmode
|dielc=1.0,
|nmstartframe=1, nmendframe=2, nminterval=1,
|maxcyc=10000, drms=0.001,
|nmode_igb=1, nmode_istrng=0.1,
|/
|--------------------------------------------------------------
|Complex topology file: ../complex.parmtop
|Receptor topology file: ../protein.parmtop
|Ligand topology file: ../ligand.parmtop
|Initial mdcrd(s): ../../centering/prod_cen_strip_sol_ion.mdcrd
|
|Best guess for receptor mask: ":1-189"
|Best guess for ligand mask: ":190"
|Ligand residue name is "MGO"
|
|Calculations performed using 2 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).
-------------------------------------------------------------------------------
Well so what could be the possible reason? Can someone please help me
out with both these issues.
1) The long time for NMODE calculation with MMPBSA.py and
2) The Index error.
Thank you,
Dilraj.
> Message: 5
> Date: Fri, 14 Sep 2012 16:54:37 +0800
> From: Dilraj LAMA <dilrajl.bii.a-star.edu.sg>
> Subject: [AMBER] NMODE calculation using mmpbsa.py
> To: amber.ambermd.org
> Message-ID:
> <20120914165437.160673zz3c9psjwt.webmail.bii.a-star.edu.sg>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> Dear Amber users,
> I am trying to use the python script for MMPBSA
> calculation. As a test, I am running the calculation on two snapshot
> from my trajectory. The PB and GB calculation went of fine but am
> having issues with the NMODE calculation.
>
> It is taking unusually long time to perform the calculation (close to
> 10hours of CPU time)
>
> Here is my input script.
>
> --------------------------------------
> sample input file for NMODE calculation
> &general
> startframe=1, endframe=10, interval=5,
> verbose=1, keep_files=0, strip_mdcrd=0,
> /
> &nmode
> dielc=1.0,
> nmstartframe=1, nmendframe=2, nminterval=1,
> maxcyc=10000, drms=0.001,
> nmode_igb=1, nmode_istrng=0.1,
> /
> --------------------------------------
> I am using the serial version of MMPBSA.py.
>
> Its just a two frame calculation, So shouldn't take that long.
>
> Am I missing something? Will be glad if someone give me an insight.
>
> Thank you,
> Dilraj.
>
>
>
>
> Message: 7
> Date: Fri, 14 Sep 2012 07:15:28 -0400
> From: Bill Miller III <brmilleriii.gmail.com>
> Subject: Re: [AMBER] NMODE calculation using mmpbsa.py
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <E20FEF81-A83F-4FC5-8F2E-8E37B33AE0D1.gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
> Nmode calculations are very computationally demanding and could
> easily take this long depending on system size and available
> computer resources. Without knowing these details, though, it is
> difficult to assess whether this is expected or not for your
> calculation.
>
> -Bill
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Received on Sat Sep 15 2012 - 02:30:03 PDT
