Dear Amber Users,
I am setting up an Amber minimization of a small RNA molecule and have
encountered an 'integer divide by zero' error when running sander.
This is my first attempt to use amber, so I anticipate this is a dumb
mistake that can be easily rectified.
(files are located at
http://pkh.caltech.edu/public_files/
I started with input_sml.pdb, which is a 4-nt RNA sequence without
hydrogens. I reviewed the structure in VMD and nothing struck me as
being structurally incorrect.
I used leap to generate topology/crd files:
>source leaprc.ff99SB
>source leaprc.rna.ff99
>loadamberparams frcmod.tip4pew
>WAT=TP4
>mol = loadpdb input_sml.pdb
>addions2 mol Na+ 0.
>solvatebox mol TIP4PEWBOX 12.0
>saveamberparm mol input_sml.parm input_sml.crd
On a side, loading rna.ff99 generated messages like
...
Substituting map H4* -> H4' for H4* -> H4'
Substituting map H3* -> H3' for H3* -> H3'
Substituting map H1* -> H1' for H1* -> H1'
Substituting map H2*1 -> H2'1 for H2*1 -> H2'1
...
but I am not sure if this is of any consequence.
Leap seemed to execute without any errors, aside from bond length
warnings about the TIP4 water and messages about improper torsions
(which don't seem to be an issue for my structure)
Minimization via sander invariably fails due to an integer divide by
zero error. My input file contains the following:
...
Minimisation of PP in solution
&cntrl
imin=1, maxcyc=200,
ntpr=5,cut=8.0,
ntr=1,
&end
Group in put for restraint
1.0
RES 1 75
END
END
...
and I run the code via
...
sander -i min_sml.inp -o min_sml.out -p input_sml.parm -c
input_sml.crd -r restrt_sml -ref input_sml.crd
...
Amber gracefully dies with:
...forrtl: severe (71): integer divide by zero
Image PC Routine Line
Source
sander 0000000000A9D29C Unknown Unknown Unknown
sander 0000000000A9731D Unknown Unknown Unknown
....
Any help with this issue would be much appreciated!
best
pete
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Received on Sat Sep 25 2010 - 10:30:07 PDT
