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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 6
Date: Sat, 29 Aug 2015 07:22:42 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] Segmentation Fault with pmemd
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAEk9e3qw=RA2PD=v3O5dbZOy45mFOLU0krTj7SOd=5JX7RvDVg.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
On Sat, Aug 29, 2015 at 4:02 AM, Ziheng Wang <zihengwang.sps.edu> wrote:
> Hi all,
>
> I am simulating a small protein system with a Mg2+ GTP bound (Mg2+ params
> from frcmod.) I am using frcmod.ionslm_1264_tip3p for metal parameters and
> http://www.pharmacy.manchester.ac.uk/bryce/amber/ for GTP parameters. I
> was able to generate prmtop and inpcrd for the system. However, I get this
> error message when running pmemd.cuda:
> Program received signal SIGSEGV: Segmentation fault - invalid memory
> reference.
>
> Backtrace for this error:
> #0 0x7FEFF8B0C7D7
> #1 0x7FEFF8B0CDDE
> #2 0x7FEFF8247FEF
> #3 0x46DB1A in __mol_list_mod_MOD_setup_molecule_lists
> #4 0x4AE5F0 in __pme_alltasks_setup_mod_MOD_pme_alltasks_setup
> #5 0x492034 in MAIN__ at pmemd.F90:?
> /tmp/slurmd/job07160/slurm_script: line 27: 19155 Segmentation fault
> (core dumped)
>
> The output file stops after line Energy averages sample interval:
> | ene_avg_sampling = 1000
> with no error message.
>
> The md input file is:
>
> &cntrl
> imin = 0, nstlim = 100000, dt = 0.001,
> irest = 0, ntx = 1, ig = 45678,
> tempi = 100.0, temp0 = 298.0,
> ntc = 2, ntf = 2, tol = 0.00001,
> tautp = 0.1, taup = 0.1,
> ntwx = 1000, ntwe = 0, ntwr = 1000, ntpr = 1000,
> cut = 8.0, iwrap = 1,
> ntt =1, ntb = 1, ntp = 0,
> nscm = 0,
> ntr=1, restraintmask="!:WAT & !.H=", restraint_wt=100.0
> nmropt=1,
> ?
>
?You are using the 12-6-4 parameters for the metal ions, but you are not
using the 12-6-4 potential. Make sure you set lj1264=1 in the &cntrl
section. Also, these restraints are VERY strong. Consider values ~1 to 2
orders of magnitude smaller when running dynamics.
?
> ?
>
> &end
> &wt
> TYPE="TEMP0", istep1=0, istep2=100000,
> value1=100., value2=298.,
> &end
> &wt
> TYPE="END",
> &end
> /
>
> The system is able to minimize fine with pmemd. The same error occurs
> during MD when I run pmemd without cuda.
>
?It would help to know what your submission script looked like. Make sure
you are running pmemd.MPI for parallel instead of pmemd (pmemd is for
serial, only).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 7
Date: Sat, 29 Aug 2015 07:38:01 -0400
From: David A Case <david.case.rutgers.edu>
Subject: Re: [AMBER] How do I study the dimerisation energy (i.e.
energy required to form a dimer from two monomeric units) using AMBER?
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20150829113801.GC10287.scarletmail.rutgers.edu>
Content-Type: text/plain; charset=us-ascii
On Sat, Aug 29, 2015, Suchetana Gupta wrote:
> My protein is a homodimer of some ~100 amino acids. I wish to calculate its
> energy required for dimerisation. The process that I am following is:
> 1. Take the dimer. Run 40ns MD. Calculate MMGBSA free energy.
> 2. Take a monomer. Run 40ns MD. Calculate MMGBSA free energy.
> Dimerisation energy=1-(2*2)
This sounds correct to me. Make sure that you are including an estimate of
the configurational entropy for both calculations.
>
> Now doing this, I am getting less dimerisation energy for a wild type
> protein than the drug resistant mutant one.
Do you know if this is right or wrong (i.e. compared to experiment)? If the
drug binds in the dimer interface, then your result would be consistent with
the mutant having drug resistance (since the binding pocket is less exposed
in the mutant than in the WT protein.)
> Moreover, the drug resistant variety (both monomer as well as dimer) is
> showing stabler energy value than WT counterpart.
You cannot compare (say) the free energy of the WT monomer with that of the
mutant monomer. They are not isomers of each other, and hence molecular
mechanics gives no information about their free energy difference.
A more accurate calculation (at least in principle) would be to use TI to
mutate the WT into the mutant sequence. Do this twice: once in the monomer,
and once in the dimer, and construct a thermodynamics cycle to generate
relative binding free energies.
...dac
------------------------------
Message: 8
Date: Sat, 29 Aug 2015 07:42:34 -0400
From: David A Case <david.case.rutgers.edu>
Subject: Re: [AMBER] Segmentation Fault with pmemd
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20150829114234.GD10287.scarletmail.rutgers.edu>
Content-Type: text/plain; charset=us-ascii
On Sat, Aug 29, 2015, Ziheng Wang wrote:
>
> I am simulating a small protein system with a Mg2+ GTP bound (Mg2+
> params from frcmod.) I am using frcmod.ionslm_1264_tip3p for metal
> parameters and http://www.pharmacy.manchester.ac.uk/bryce/amber/ for
> GTP parameters. I was able to generate prmtop and inpcrd for the
> system. However, I get this error message when running pmemd.cuda:
> Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
>
> The system is able to minimize fine with pmemd. The same error occurs
> during MD when I run pmemd without cuda.
Usual debugging advice: set nstlim to some small value (say 100), and ntpr and
ntwx to 1. See what happens (use the CPU version in serial). Is the energy
at the start of MD the same as at the end of minimization? Does it fail on
the first step or later? If later, look at the structures in the mdcrd file
to see if you can find problems.
....dac
------------------------------
Message: 9
Date: Sat, 29 Aug 2015 05:39:10 -0700
From: Martina Devi <martinadevi2011.gmail.com>
Subject: Re: [AMBER] mismatch base pair from nab
To: david.case.rutgers.edu, AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CA+JOZ38=tYLkN4KGgixRJPWzCfwmBorrYx3-LEqeV9YubgsrPw.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Thank you to both of you sir. The matter was that I did not remove the
atoms that was not suppose to be there. So the pdb that was generated
should be edited with the atoms that should not be present in the modified
residue.
Martina
On Tue, Aug 25, 2015 at 12:57 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Tue, Aug 25, 2015, Martina Devi wrote:
> >
> > I did not get any error message.The base which I did not edit can be
> viewed
> > in xleap The desired edited base which I want to load cannot be viewed in
> > xleap.
>
> Can you be more specific about what you mean by "cannot be viewed in
> xleap"?
> What were the exact commands you typed, and what was the exact response
> from
> the program?
>
> Don't restrict your reporting to what you think are "error messages". In
> order to help, we need to know everything that happened.
>
> >
> > What I did was I made two pdb files. Then I edited the required portion
> and
> > copied from the other pdb. Is this technique correct?
>
> Remember that you must remove any atoms in your modified residue that are
> not
> supposed to be there: all atoms present in the PDB file must also be in the
> library file for the modified residue.
>
> ....dac
>
>
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>
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Received on Sun Aug 30 2015 - 07:30:02 PDT