AMBER Archive (2008)

Subject: Re: AMBER: F modified RNA is split in two parts when running sander simulated annealing

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Wed Oct 01 2008 - 04:56:38 CDT

Hi,
> ===============================================================================
>
> NSTEP = 11938 TIME(PS) = 5.969 TEMP(K) =431725.07 PRESS = 0.0
> Etot = NaN EKtot = 1562702.1324 EPtot = NaN
> BOND = 977.0778 ANGLE = 1738.1119 DIHED = 1303.8070
> 1-4 NB = 431.4051 1-4 EEL = -4741.3679 VDWAALS = -668.7301
> EELEC = 3396.5918 EGB = NaN RESTRAINT = 160.1925
> EAMBER (non-restraint) = NaN
> ------------------------------------------------------------------------------
...Since here only EGB is broken I guess the underlying problem is an
effectove Born radius becoming <= zero.

You mention that this is more likely at higher temperatures, so
this probably happens when some atoms get very close (closer than
Lennard-Jones repulsion or a bond between them would allow at 300K).

Since this happens with Flourine-modified DNA I further guess that
the Flouride (GB-)parameters are part of the problem.

I hope this guesswork helps,
good luck
Andreas

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