Re: [AMBER] CUDA install fails due to undefined netcdf definitions

From: Matthew Wampole <Matthew.Wampole.jefferson.edu> Date: Thu, 6 Jun 2013 21:12:10 +0000 · > Hi Amber users,

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
------------------------------
Message: 36
Date: Thu, 6 Jun 2013 11:56:40 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] MMPBSA.py Error
To: Senthil Natesan <sen.natesan.yahoo.com>,    AMBER Mailing List
        <amber.ambermd.org>
Message-ID:
        <CAEk9e3rF1ZosiR2xSqoEBnZgPXNTBwSOVjsuX=28BJxTjuSnAg.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
On Thu, Jun 6, 2013 at 11:46 AM, Senthil Natesan <sen.natesan.yahoo.com>wrote:
> Dear Amber Users,
>
> I am trying to do MMPBSA calculations with a single trajectory and gives
> the following error:
>
> ----------------------------------------------
>
> Preparing trajectories for simulation...
> Error in box coord line of trajectory h3_820_complex_prod2.mdcrd.
>       Expect only 3 or 6 box coords.
> Problem line:   4.509  71.808  82.630  27.602  29.349  36.456  58.340
> 102.059 -20.666
>
>     Error: Could not set up h3_820_complex_prod2.mdcrd for reading.
> Error: trajin: Could not set up trajectory.
> TrajError: Trajectory h3_820_complex_prod2.mdcrd has 0 frames!
> Exiting. All files have been retained.
> --------------------------------------------------
>
> I went through the previous user lists messages, but there is no clear
> answers that I could find.
>
These error messages indicate that your trajectory file is incompatible
with the topology file it is paired with.  As always with MM/PBSA-type
analyses, simple debugging starts with visualizing the problematic
trajectory (either the input trajectories or the intermediate ones with the
names like _MMPBSA_*.mdcrd.# or _MMPBSA_*.nc.#).  If the files are
incompatible, it will be immediately obvious.
Note the beginning of the MMPBSA.py chapter suggests that you should be
able to run MMPBSA analyses 'by hand' to avoid treating these scripts like
a black box.  When you can do this, it becomes much easier to debug issues
(or avoid them in the first place!) with MMPBSA.py
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
------------------------------
Message: 37
Date: Thu, 6 Jun 2013 14:11:01 -0400
From: "me, Nancy" <bwan0408.gmail.com>
Subject: [AMBER] PM6 and PM3
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAOkVv_Bh_ie1Rq899ZQSXW4OEn3zn=4t=UkwaqqxuDJ1NcC9UA.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
I am running a QM/MM simulation for the system that contains a hexose
molecule, a hydronium molecule and water molecules. The hexose and
hydronium molecules are in the QM region and water molecules are in the MM
region. When I run it with PM6, I found there is hydrogen atom exchange
between that on hydroxyl groups of hexose and on hydronium molecule, but
when I run the system with PM3, there is no hydrogen atom. I wonder if this
is a bug in PM6. Is there any way to avoid the hydrogen exchange using PM6?
Thanks.
------------------------------
Message: 38
Date: Thu, 6 Jun 2013 14:34:11 -0400
From: Brian Radak <radak004.umn.edu>
Subject: Re: [AMBER] PM6 and PM3
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAJrka9y9TxfYY7CQd9vFSS+paeWCnkpRJv4QJJHYdvu0nx8WzQ.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
This is probably not a bug and can probably not be avoided without changing
your simulation protocol.
PM3 and PM6 are quite different model quantum chemistries and there is no
reason to believe their behavior should be qualitatively identical (it goes
without saying that they will be quantitatively different). I doubt that
this "exotic" behavior with PM6 is due to an error in its implementation.
Such a difference is likely either a natural "error" of the model
(*i.e.*predicted behavior that is not physically accurate) or else an
artifact of
your simulation protocol (*i.e. *some stochastic element of the sampling
protocol has caused the samples to diverge). Can you describe more what
your simulation protocol is?
With *any* semi-empirical quantum method, it is probably a good idea to
validate by comparing to a respectable level of *ab initio* theory. It is
of course up to you and a referee as to what is compared. In this case I
would look at proton affinities, but that is just my opinion.
Regards,
Brian
On Thu, Jun 6, 2013 at 2:11 PM, me, Nancy <bwan0408.gmail.com> wrote:
> I am running a QM/MM simulation for the system that contains a hexose
> molecule, a hydronium molecule and water molecules. The hexose and
> hydronium molecules are in the QM region and water molecules are in the MM
> region. When I run it with PM6, I found there is hydrogen atom exchange
> between that on hydroxyl groups of hexose and on hydronium molecule, but
> when I run the system with PM3, there is no hydrogen atom. I wonder if this
> is a bug in PM6. Is there any way to avoid the hydrogen exchange using PM6?
> Thanks.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
 Brian Radak                                             :     BioMaPS
Institute for Quantitative Biology
 PhD candidate - York Research Group       :     Rutgers, The State
University of New Jersey
 University of Minnesota - Twin Cities         :     Center for Integrative
Proteomics Room 308
 Graduate Program in Chemical Physics     :     174 Frelinghuysen Road,
 Department of Chemistry                          :     Piscataway, NJ
08854-8066
 radak004.umn.edu                                 :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
------------------------------
Message: 39
Date: Thu, 6 Jun 2013 14:55:25 -0400
From: "me, Nancy" <bwan0408.gmail.com>
Subject: Re: [AMBER] PM6 and PM3
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAOkVv_CmdJ=BPsyMa0g3_nyFJPpysO8yjxxHHJEfxo0RYWfEhQ.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
I was just running normal NPT QM/MM dynamics without any biased sampling. I
used the same initial configurations and velocities. The only difference is
the QM theory. The hydrogen exchange on the hydroxyl group with hydronium
hydrogen happened very fast with PM6, which is not likely it should be.
On Thu, Jun 6, 2013 at 2:34 PM, Brian Radak <radak004.umn.edu> wrote:
> This is probably not a bug and can probably not be avoided without changing
> your simulation protocol.
>
> PM3 and PM6 are quite different model quantum chemistries and there is no
> reason to believe their behavior should be qualitatively identical (it goes
> without saying that they will be quantitatively different). I doubt that
> this "exotic" behavior with PM6 is due to an error in its implementation.
>
> Such a difference is likely either a natural "error" of the model
> (*i.e.*predicted behavior that is not physically accurate) or else an
> artifact of
> your simulation protocol (*i.e. *some stochastic element of the sampling
> protocol has caused the samples to diverge). Can you describe more what
> your simulation protocol is?
>
> With *any* semi-empirical quantum method, it is probably a good idea to
> validate by comparing to a respectable level of *ab initio* theory. It is
> of course up to you and a referee as to what is compared. In this case I
> would look at proton affinities, but that is just my opinion.
>
> Regards,
> Brian
>
>
> On Thu, Jun 6, 2013 at 2:11 PM, me, Nancy <bwan0408.gmail.com> wrote:
>
> > I am running a QM/MM simulation for the system that contains a hexose
> > molecule, a hydronium molecule and water molecules. The hexose and
> > hydronium molecules are in the QM region and water molecules are in the
> MM
> > region. When I run it with PM6, I found there is hydrogen atom exchange
> > between that on hydroxyl groups of hexose and on hydronium molecule, but
> > when I run the system with PM3, there is no hydrogen atom. I wonder if
> this
> > is a bug in PM6. Is there any way to avoid the hydrogen exchange using
> PM6?
> > Thanks.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ================================ Current Address =======================
>  Brian Radak                                             :     BioMaPS
> Institute for Quantitative Biology
>  PhD candidate - York Research Group       :     Rutgers, The State
> University of New Jersey
>  University of Minnesota - Twin Cities         :     Center for Integrative
> Proteomics Room 308
>  Graduate Program in Chemical Physics     :     174 Frelinghuysen Road,
>  Department of Chemistry                          :     Piscataway, NJ
> 08854-8066
>  radak004.umn.edu                                 :
> radakb.biomaps.rutgers.edu
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
------------------------------
Message: 40
Date: Thu, 6 Jun 2013 18:59:25 +0000
From: Amparo Garcia Lopez <Amparo.GarciaLopez.unige.ch>
Subject: [AMBER] unable to run minimizations after new installation of
        amber11
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <6EDA80B84ADD0244916372CCED8D9C5F5A7CAF.hotel.isis.unige.ch>
Content-Type: text/plain; charset="iso-8859-1"
Dear all,
We recently made a new installation of amber11 from scratch with ambertools1.5 incl the bugfix.all. Although most of the tests I've run so far work well (xleap and MD production with pmemd), I have this problem with all the minimization/equilibration tests I've run with pmemd. This is 21-nt RNAs I'm running, with explicit solvent.
I've tried different crd and top files, all of which would work well in the past using the same scripts im using now, but each of them give me this error since the new installation:
----
At line 109 of file inpcrd_dat.f90 (unit = 9, file = 'TSL2_1N8R.wat.min1')
Fortran runtime error: End of file
  Unit    9 Error on OPEN: TSL2_1N8R.wat.min2
STOP PMEMD Terminated Abnormally!
----
then I get this fort.16 file. The file TSL2_1N8R.wat.min1 is in blank. the .out files do not give any clue as to why pmemd stopped, and I really dont know what this means. this is what I run:
min1.in:
Min of just waters
 &cntrl
        imin=1, maxcyc=5000, ncyc=100, drms=0.5, ibelly=1,
        ntb=1,
 &end
Atoms that are going to move in the minimization
RES 22 7000
END
END
min2.in:
Min of all
 &cntrl
        imin=1, maxcyc=5000, ncyc=50, drms=0.2,
        ntb=1,
 &end
md1.in:
 &cntrl
  ntf=2, ntb=2,
  iwrap=1,
  ntr=1,
  nstlim=20000,dt=0.001,
  temp0=100, ntt=1,
  ntp=1,
  ntc=2,
 &end
Restrain DNA,counterions
100.0
RES 1 69
END
END
etc etc
I've tried to find a similar error on previous mails from the amber list, but in all the cases I found, it came together with other error messages.
http://archive.ambermd.org/201204/0027.html
http://archive.ambermd.org/201108/0198.html
I apologise because this is probably something very obvious, and I know it looks like a problem with my files, but I'm lost because it's exactly the same scripts, and the same topologies and coordinates I was running before (and not just for one molecule, I've tried three).
Thanks very much in advance for any ideas.
Amparo Garcia-Lopez, Ph.D.
Pharmaceutical Biochemistry
School of Pharmaceutical Sciences
University of Geneva
Quai Ernest-Ansermet 30
1211 Gen?ve 4 - Switzerland
Tel:  +41 (0)22 379 3376
Fax: +41 (0)22 379 3360
e-mail: Amparo.GarciaLopez.unige.ch
------------------------------
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