Re: [AMBER] NMODE list index out of range error

From: Jason Swails <jason.swails.gmail.com>
Date: Sat, 28 Jan 2012 10:42:42 -0500

Can you send your _MMPBSA_*_nm.out files so I can take a look at them?

It appears that for some reason one of the snapshots didn't minimize completely and so there are different numbers of frames for the complex receptor and ligand. However, MMPBSA should have exited more gracefully or readjusted silently.

It may also be the case that no snapshot could minimize enough for the complex or receptor or something, so there was no data to analyze. Again, the error reporting should be better.

All the best,
Jason

--
Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Jan 28, 2012, at 1:43 AM, Sangeetha B <sangeetha.bicpu.edu.in> wrote:
> 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?
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jan 28 2012 - 08:00:03 PST
Custom Search