AMBER Archive (2008)

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

From: Peter Podbevšek (Peter.Podbevsek_at_ki.si)
Date: Thu Oct 02 2008 - 08:08:51 CDT

Andreas thank you for replying. I'm kind of new at this so all the fluorine parameters look fine to me. I got the partial charger from literature and all the other parameters were already included in the force field. Are there some special parameters for GB that I'm missing?
I did some more experimenting and found out that the problem is somehow related to the electrostatic terms of the potential function (with a 0.1 weight on ELEC simulations finish without problems).

Here is an image of the problematic molecule if it looks familiar to someone. This happens on a timescale of around 100 fs.
http://www2.arnes.si/~ssdppodb/amber.jpg

Regards
Peter

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Andreas Svrcek-Seiler
Sent: Wednesday, October 01, 2008 11:57 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: F modified RNA is split in two parts when running sander simulated annealing

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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