Hi David,
How old is considered old? I have Amber 10 from 2008 (?) compiled on a
linux 64 bit kernel:
Linux cluster.mccammon.ucsd.edu 2.6.18-53.1.14.el5 #1 SMP Wed Mar 5
11:37:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux
I did just try recreating the parm/crd files using leap WITHOUT the
RNA FF and obtained the same result. I will try your other suggestions
to see if this improves things any. I did notice that the VDW
potential is whacky in my simulation:
> sander -i min.inp -p input.parm -c input.crd -r restrt -ref input.crd
NSTEP ENERGY RMS GMAX NAME NUMBER
10 1.2274E+10 6.6912E+08 1.7085E+11 C3' 1945
BOND = 92593.0046 ANGLE = 6364.2650 DIHED = 1729.5378
VDWAALS = ************* EEL = -224802.7617 HBOND = 0.0000
1-4 VDW = 3763103.9162 1-4 EEL = -7773.3675 RESTRAINT = 0.0097
EAMBER = *************
Thanks for getting back to me and I will try a few other tweaks to get
this running.
Best
pete
On Mon, Sep 27, 2010 at 6:43 AM, case <case.biomaps.rutgers.edu> wrote:
> On Sat, Sep 25, 2010, Pete Kekenes-Huskey wrote:
>
>> I am setting up an Amber minimization of a small RNA molecule and have
>> encountered an 'integer divide by zero' error when running sander.
>
>> >source leaprc.rna.ff99
>
> Looks like you have an old version of Amber (which version is it? what
> compiler and OS?), since this "rna" file is no longer needed, and has been
> moved to the "oldff" location, only to be used for those who need backward
> compatibility).
>
> I can't reproduce your result...I ran your system with exactly your input
> files, and everything looked fine. Maybe an upgrade will help; maybe not
> loading both leaprc.ff99SB and leaprc.rna.ff99 would help. You can try to
> play with things to see what triggers the error (is it RNA vs DNA? TIP4P vs.
> TIP3P water? etc.) Integer divide by zero is an error I don't recall having
> seen before...
>
> ....dac
>
>
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Received on Mon Sep 27 2010 - 07:30:06 PDT
