Thanks for the response, but this doesn't solve my problem. I still get the
exact same error.
I have linked leaprc.ff14SB as my default leaprc. I understand this is
recommended usage?
I also tried sourcing the frcmod file directly before. Did not seem to make
any difference.
I do not understand what 'set default PBradii mbondi2' is all about. Is
this absolutely necessary? If so, why?
I hope to add solvent (sovateoct 1vom TIP3PBOX 8.0) in the next step but I
think I should be able to run a protein+ion minimization in vacuum to begin
with.
I actually tried adding the solvent before, that also doesn't work (with
ntb=1) with another error (Error: peek_ewald_inpcrd: SHOULD NOT BE HERE)
but I figured I should go step-by-step.
I did work on this a full day before asking help on the mail list. :)
Regards,
Murat
On Tue, May 13, 2014 at 10:46 PM, Ilyas Yildirim <
i-yildirim.northwestern.edu> wrote:
> The problem is the following line in your leap script:
>
> ions = loadamberparams frcmod.ionsjc_tip3p
>
> Load the frcmod file directly. Here is a sample script that should give
> you some directions:
>
> -------------- xleap.in ------------------
> source leaprc.ff10
> loadamberparams frcmod.ionsjc_tip3p
> set default PBradii mbondi2
> 1vom = loadpdb 1vom-clean.pdb
> addions 1vom Na+
> saveamberparm 1vom prmtop inpcrd
> ------------------------------------------
>
> Just do not forget to solvate the system with water molecules which
> otherwise won't mean anything (except studying behavior of 1vom in Na+/Cl-
> environment).
>
> Ilyas Yildirim, Ph.D.
> -----------------------------------------------------------
> = Department of Chemistry - 2145 Sheridan Road =
> = Northwestern University - Evanston, IL 60208 =
> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
> = Website : http://ilyasyildirim.wordpress.com =
> = ------------------------------------------------------- =
> = http://www.linkedin.com/in/yildirimilyas =
> = http://scholar.google.com/citations?user=O6RQCcwAAAAJ =
> -----------------------------------------------------------
>
>
> On Tue, 13 May 2014, MURAT OZTURK wrote:
>
> > Hey everybody,
> >
> > I have some experience with gromacs and lammps, but we just got some new
> > GPUs and decided to give amber a try to see how it performs.
> >
> > I am having difficulty setting up a simple system.
> >
> > I have a molecule from pdb, which I cleaned up properly.
> >
> > First I do this at leap
> >
> > 1vom = loadpdb 1vom-clean.pdb
> > saveamberparm 1vom prmtop inpcrd
> >
> > then I minimize this (in vacuum) using
> >
> > &cntrl
> > imin = 1,
> > maxcyc = 2500,
> > ncyc = 1000,
> > ntb = 0,
> > ntr = 0,
> > cut = 10.0,
> > /
> >
> > which works fine.
> >
> > Then I add ions by doing exactly this in tleap.
> >
> > addions 1vom Na+ 0
> > ions = loadamberparams frcmod.ionsjc_tip3p
> > saveamberparm 1vom prmtop inpcrd
> >
> > Using the same minimization script, I get this error :
> >
> > At line 842 of file ew_box.F90 (unit = 9, file = 'inpcrd')
> > Fortran runtime error: End of file
> >
> > As a newbie, this error is very opaque to me, as I have no idea what is
> > going on. I would appreciate any help to understand what i am missing.
> >
> > Regards,
> > Murat
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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>
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Received on Tue May 13 2014 - 13:30:02 PDT
