Thank you very much for clarification. The bug explains the inconsistency I
was 'sensing' in the files. I have NATOMS 86347 and then 43150 lines, for
example. I will be recompiling in the morning. How would I make sure the
patch is upstream?
I can hack C/C++ but I am hopeless with FORTRAN, thanks for the format
information too.
By the way, I am not at all interested in vacuum minimization, I just don't
see why it shouldn't work. It should run, at least until it explodes or
something, it is merely meant as a sanity check on my side.
As for placing ions, I find it preferable to have some concentration of
ions rather than the mere number of ions required to neutralize the system.
Given that, random placement is fine, so addionsrand use is preferable.
Thanks for that tip too.
Regards,
Murat
On Wed, May 14, 2014 at 1:16 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Tue, May 13, 2014 at 4:47 PM, MURAT OZTURK <murozturk.ku.edu.tr> wrote:
>
> > Thanks for the response.
> >
> > Yes, I am sure that I am using ntb = 0. I also know that it works prior
> to
> > adding ions, so adding ions is what breaks it.
> >
>
> Yikes... Don't do this ;). If you plan on running with explicit solvent,
> do this off the bat. (pmemd.cuda doesn't even support vacuum dynamics).
> The best way to add ions to a system via tleap is actually to add the
> solvent first and then replace random solvent molecules with ions (at least
> IMO -- YMMV). So something like this:
>
> system = loadPDB you_system.pdb
> ions = loadAmberParams frcmod.ionsjc_tip3p
> solvateOct system TIP3PBOX 15.0
> addIonsRand system Na+ 0
> saveAmberParm system your_system.parm7 your_system.rst7
>
> The first line loads your system. The second loads the ion parameters (as
> Ilyas mentioned, the "ions=" part is optional). The third solvates the
> system with TIP3P waters in a truncated octahedron with at least a 15
> Angstrom buffer around the solute. The fourth replaces enough waters with
> sodium ions to neutralize the system. The last saves your topology file.
> (Of course this assumes a default leaprc file, which you mentioned you
> had.)
>
>
> > Interestingly, the last two lines of the inpcrd of the protein only
> system
> > reads
> >
> > 82.4450000 14.3940000 -13.6870000 81.7180000 15.3700000 -13.4430000
> > 83.6048830 14.5521392 -13.3126966
> >
> > whereas the inpcrd with ions reads
> >
> > 86.3470000 12.2630000 -15.2900000 87.2459461 11.6555756 -15.3950273
> > 86.5023142 13.2275008 -15.7734415 86.1831237 12.5406017 -13.8148107
> > 87.2007
>
>
> > This does not look correct to me. But it is purely generated by leap.
> >
>
> Looks like you got clipped with a bug we recently found (LEaP occasionally
> truncates files). An update should be posted tomorrow morning (EST in the
> USA) -- here is the relevant thread on the mailing list describing the bug
> http://archive.ambermd.org/201404/0532.html (there is a proposed patch
> attached there that you can download and apply if you don't want to wait).
>
> Why are there 6 columns in the first place? I'd expect 3 columns *
> > numberOfAtoms rows. Forgive my gromacs inclination, is this the amber
> way?
> >
>
> Yes -- this is the amber way. It is the x, y, z coordinates of two atoms.
>
>
> > (CRD spec states FORMAT(6F12.7), which is again cryptic to me.)
> >
>
> This is a Fortran format statement. It indicates that there are at most 6
> Floating point numbers per line, each with 7 decimal points that take up
> exactly 12 characters. Amber is traditionally a Fortran code-base
> (exclusively back in the early days of Amber 3 to 4, although it is FAR
> more diverse now). You can still see strong remnants of this Fortran
> heritage everywhere.
>
> And in the last one, there is a row with a single column. Is this supposed
> > to happen?
> >
>
> No. It's a bug that should hopefully have a fix posted soon (see above).
>
>
> >
> > Regards,
> >
> > Murat
> >
> >
> >
> > Here is the full(ish) output including the error. :
> >
> > [snip]
> >
> >
> --------------------------------------------------------------------------------
> > 1. RESOURCE USE:
> >
> >
> --------------------------------------------------------------------------------
> >
> > | Flags:
> >
> > | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
> > At line 842 of file ew_box.F90 (unit = 9, file = 'inpcrd')
> > Fortran runtime error: End of file
> >
>
> You got hit by the leap bug -- the file was truncated.
>
> Hope this helps,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> AMBER.ambermd.org
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>
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Received on Tue May 13 2014 - 16:30:02 PDT
