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
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Received on Tue May 13 2014 - 13:00:02 PDT
