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From: Jason Swails <jason.swails.gmail.com>

Date: Tue, 1 Dec 2015 08:19:25 -0500

On Tue, Dec 1, 2015 at 7:13 AM, Atila Petrosian <atila.petrosian.gmail.com>

wrote:

*> Dear amber users,
*

*>
*

*> I am doing mmgbsa calculations on my protein-ligand systems using
*

*> ambertools 14 based on tutorial in amber web site.
*

*>
*

*>
*

*> ------------------------------------------------------------------------------------
*

*> When I used follwing state, I obtained output file without any problem.
*

*>
*

*> Input file for running GB without quasi-harmonic entropy calculation is as
*

*> follows:
*

*>
*

*> &general
*

*> startframe=2000, endframe=4000, interval=5,
*

*> verbose=1, keep_files=1,
*

*> entropy=0,
*

*> /
*

*> &gb
*

*> igb=2, saltcon=0.100,
*

*> /
*

*>
*

*>
*

*> ------------------------------------------------------------------------------------
*

*> But, When I used follwing state:
*

*>
*

*> Input file for running GB with quasi-harmonic entropy calculation is as
*

*> follows:
*

*>
*

*> &general
*

*> startframe=2000, endframe=4000, interval=5,
*

*> verbose=1, keep_files=1,
*

*> entropy=1,
*

*> /
*

*> &gb
*

*> igb=2, saltcon=0.100,
*

*> /
*

*>
*

*> I encountered with following error:
*

*>
*

*> Running calculations on normal system...
*

*>
*

*> Beginning GB calculations with
*

*> /share/apps/amber/amber14/bin/mmpbsa_py_energy
*

*> calculating complex contribution...
*

*> calculating receptor contribution...
*

*> terminate called after throwing an instance of 'std::bad_alloc'
*

*>
*

It looks like you ran out of memory for the quasi-harmonic calculation.

But, When I used follwing state:

*>
*

*> Input file for running entropy calculations using NMode is as follows:
*

*>
*

*> &general
*

*> startframe=2000, endframe=4000, interval=5,
*

*> verbose=1, keep_files=1,
*

*> /
*

*> &nmode
*

*> nmstartframe=1, nmendframe=400, nminterval=4,
*

*> nmode_igb=1, nmode_istrng=0.1, maxcyc=1000, drms=0.01,
*

*> /
*

*>
*

maxcyc=1000 is almost certainly not enough to minimize most snapshots

sufficiently for normal mode calculations.

*> I encountered with following error:
*

*>
*

*> Running calculations on normal system...
*

*>
*

*> Beginning nmode calculations with
*

*> /share/apps/amber/amber14/bin/mmpbsa_py_nabnmode
*

*> calculating complex contribution...
*

*> Line minimizer aborted: step at upper bound 0.0069297972
*

*>
*

This suggests that the minimizer failed. You can always try to minimize

some of these snapshots "by hand" and see if/where it gets stuck. Note

that entropy calculations are time-consuming, often tricky to get to work

correctly, and oftentimes unreliable (after all, it depends on the rigid

rotor approximation which doesn't hold as well for big squishy

proteins/RNA/DNA as it does for smaller molecules).

*> Error occured on rank 6.
*

*> Exiting. All files have been retained.
*

*>
*

*> ------------------------------------------------------------------------------------
*

*>
*

*> What means of Error occured on rank 6?
*

*>
*

You are running MMPBSA.py.MPI on at least 7 processors. The "7th"

processor is given rank 6 (the first is given rank 0). Which means that

the error occurred on the 7th processor. So the error message, if printed

to one of the output files, will print to an output file that ends with .6

HTH,

Jason

Date: Tue, 1 Dec 2015 08:19:25 -0500

On Tue, Dec 1, 2015 at 7:13 AM, Atila Petrosian <atila.petrosian.gmail.com>

wrote:

It looks like you ran out of memory for the quasi-harmonic calculation.

But, When I used follwing state:

maxcyc=1000 is almost certainly not enough to minimize most snapshots

sufficiently for normal mode calculations.

This suggests that the minimizer failed. You can always try to minimize

some of these snapshots "by hand" and see if/where it gets stuck. Note

that entropy calculations are time-consuming, often tricky to get to work

correctly, and oftentimes unreliable (after all, it depends on the rigid

rotor approximation which doesn't hold as well for big squishy

proteins/RNA/DNA as it does for smaller molecules).

You are running MMPBSA.py.MPI on at least 7 processors. The "7th"

processor is given rank 6 (the first is given rank 0). Which means that

the error occurred on the 7th processor. So the error message, if printed

to one of the output files, will print to an output file that ends with .6

HTH,

Jason

-- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Dec 01 2015 - 05:30:06 PST

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