Funny. That's actually how I started using AMBER. It was with version 4.1 and then 5.0 (when xleap was supposed to not crash anymore ... or less :-). All I remember is that I used this spreadsheet like input in xleap to do the setup. But the major problem is that I would need a parser for that.
Cheers,
Hannes.
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: 25 March 2014 14:54
To: amber.ambermd.org
Subject: Re: [AMBER] tleap cannot handle dummies in the middle?
On Tue, 2014-03-25 at 14:32 +0000, Hannes Loeffler wrote:
> The work around is to delete every bond on suspicion because deletebond
> on a non-existent bond will only result in a message on stdout and is
> thus harmless.
>
> set s.1.H pert true
> deletebond s.1.H s.1.DU6
> bond s.1.H s.1.DU6
> deletebond s.1.H s.1.DU10
> bond s.1.H s.1.DU10
> deletebond s.1.H s.1.C
> bond s.1.H s.1.C
>
> I suppose when you say pert is no longer relevant you refer to the way
> free energy calculations are now done with AMBER?
I'm not sure how familiar you are with the past of Amber/tleap (my
knowledge is quite limited). tleap can write out perturbed prmtops that
basically defines both end states in the same topology file. These
files were used by the (long deprecated) "gibbs" program to do FE
calculations. Since gibbs' deprecation, no programs in Amber support
topology files whose IFPERT pointer is set to 1.
That said, I believe I've used "set pert <atom> true" in tleap in the
past in order to convince tleap that I really _did_ want more than the
'maximum' number of bonds to an atom. I don't _think_ setting an atom's
pert flag to 1 triggers IFPERT=1 in the topology file (but I'm not 100%
positive on that).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 26 2014 - 02:00:03 PDT
