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
----- Original Message -----
From: "Fabien Cailliez" <Fabien.Cailliez.ibpc.fr>
To: "AMBER" <amber.scripps.edu>
Sent: Monday, January 17, 2005 6:34 AM
Subject: AMBER: distance restraint and file fort.35
> Dear all,
>
> I am using pmemd from amber8 to perform a restrained simulation with a
> distance restraint.
> I am using the nmropt option to do it.
> It seems to work but there is a file fort.35 which is created during the
> dynamics.
> (sander from amber8 also creates this file)
> This file seems to contain the same information as the DUMPAVE file.
> Is it normal that I get this file ? And if so, what is its utility ?
>
> Thanks in advance for your suggestion,
> Fabien
>
> My input file is :
> *************************************************************************
> ***************************** md.in *****************************
> *************************************************************************
> 100 ps MD production at constant T= 300K & P= 1Atm and coupling = 5.0
> &cntrl
> imin=0, ntx=7, ntpr=500, ntwr=500, ntwx=500, ntwe=500,
> nscm=500,
> ntf=2, ntc=2,
> ntb=2, ntp=1, tautp=5.0, taup=5.0,
> nstlim=50000, t=0.0, dt=0.002,
> cut=9.0,
> ntt=1,nmropt=1,
> irest=1
> &end
> # Distance restraint
> &wt type='DUMPFREQ', istep1=10, &end
> &wt type='END', &end
> DISANG=dist.900.in
> DUMPAVE=dist900_vs_t
>
> and the file DISANG is :
> #
> # 2 TRP CD2 37 ILE N 10
> &rst
> iat=36, 599, r1= 0.0, r2 = 9.0, r3 = 9.0, r4 = 999.0,
> rk2=50.0, rk3=50.0, ir6=0, ialtd=0,
> &end
>
> --
> __________________________________________________________________
> Fabien Cailliez Tel : 01 58 41 51 63 Laboratoire de Biochimie Théorique
> e-mail : cailliez.ibpc.fr
> IBPC 13, rue Pierre et Marie Curie 75005 Paris
> __________________________________________________________________
>
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Received on Mon Jan 17 2005 - 14:53:00 PST
