AMBER Archive (2005)

Subject: Re: AMBER: distance restraint and file fort.35

From: Fabien Cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Mon Jan 17 2005 - 09:58:03 CST

Dear Dr Duke,

Thanks for your answer.
Actually I have at the end of the simulation my DUMPAVE file and the
file fort.35 which are
perfectly identical.

Yours sincerely,
Fabien

> Fabien -
> As far as nmropt = 1 stuff goes, pmemd basically does pretty much the
> exact same things as sander 6/7. I believe there are some new input
> formats supported by sander 8 for restraints/frozen atoms, and this
> stuff is not supported by pmemd (you have to use the amber 6/7 GROUP
> input), but you are not doing this sort of thing here. So the pmemd
> nmr code is really just a port of sander code to f90, whith nmropt > 1
> features stripped out. I did not otherwise touch the stuff because it
> is convoluted, not particularly well documented, and there is not a
> complete set of regression tests. I am saying all this basically to
> put the question back in the sander court. As far as any analysis I
> can do, I have tracked through the code and it looks like a temporary
> file is being opened on unit 35; I presume the file is a temporary
> because a name was not provided, but it also looks like this file
> should be the dumpave file. Do you otherwise get the dumpave file you
> provided a name for? Anyway, whoever wrote this stuff should respond
> to this message, and the amber group should specify what is going on
> here in the doc, rewrite the code, or whatever.
> Regards - Bob Duke
> 

-- 
__________________________________________________________________
Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail : cailliez_at_ibpc.fr
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					
__________________________________________________________________

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