On Sat, Aug 08, 2009, Biswaranjan Meher wrote:
> I am equilibrating a larger protein (~1200 residues) without any solvent
> molecules. I am using AMBER10 in dual core fedora system.
>
> For the first few steps (30000), the system goes fine but after that it
> complains like the following message:
>
> At line 1238 of file _ew_box.f (unit = 9, file = 'fort.9')
> Fortran runtime error: End of file
We need more information: the program only reads the prmtop file at the
beginning of a run. Did your error happen in the middle of a run? Are you
trying a restart? This probably has something to do with the value of ntb you
are using (but I'm just guessing, since you don't really say.)
Amber can sometimes have problems with systems with no solvent: it tries to
create a "virtual box" around the system, but if the conformation of your
protein changes from its original state, the system can become larger than
the virtual box. You might try setting igb=6, ntb=0, which avoids the
"virtual box" problems. Of course, also look at your structure to see if
unwanted changes are occurring.
[This dicussion avoids the thorny question of why you are trying to simulate
a 1200 residue protein in the absence of solvent in the first place: is this
really going to lead to something useful? Have you done similar simulations
with proteins 1/10 as big, for example?]
...dac
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Received on Wed Aug 19 2009 - 20:59:12 PDT
