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 =
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http://scholar.google.com/citations?user=O6RQCcwAAAAJ =
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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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Received on Tue May 13 2014 - 13:00:03 PDT
