Many thanks for all of you who tried to help me.
I have finally resolved the problem
by "try-and-error" method, of course using some information from
Amber manual.
Please find below the correct variant of the input file.
Hope the file could be useful for other amber users.
All the best,
Michael
protein restraint, heating 50K
&cntrl
imin=0,
ntx=1,
irest=0,
ntc=2,
ntf=2,
tol=0.0000001,
nstlim=50000,
ntt=3,
gamma_ln=1.0,
ntr=1,
ig=-1,
ntpr=100,
ntwr=10000,
ntwx=100,
dt=0.002,
nmropt=1,
ntb=1,
ntp=0,
cut=10.0,
ioutfm=1,
ntxo=2,
/
&rst
restraint = "distance( (5716) (6163) )"
restraint = "distance( (1297) (6163) )"
restraint = "distance( (5756) (6163) )"
restraint = "distance( (5348) (6163) )"
restraint = "distance( (5134) (6163) )"
restraint_wt = 50.0
/
&wt
type='TEMP0',
istep1=0,
istep2=50000,
value1=0.0,
value2=50.0 /
&wt type='END' /
Hold protein fixed
10.0
RES 1 509
END
END
________________________________
From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
Sent: Monday, February 20, 2017 3:58 PM
To: amber.ambermd.org
Subject: Re: [AMBER] error in the input file
On Mon, 20 Feb 2017 12:47:03 +0000
Michael Shokhen <michael.shokhen.biu.ac.il> wrote:
> Dear Amber experts,
>
>
> Computer reports error in my input file for MD run.
>
> I need your help how to correct my input file.
>
> See details below.
>
>
> Thank you,
>
> Michael
>
>
> Input file: heat1.in
>
>
> protein restraint, heating 50K
>
> &cntrl
>
> imin=0,
>
> ntx=1,
>
> irest=0,
>
> ntc=2,
>
> ntf=2,
>
> tol=0.0000001,
>
> nstlim=50000,
>
> ntt=3,
>
> gamma_ln=1.0,
>
> ntr=1,
>
> ig=-1,
>
> ntpr=100,
>
> ntwr=10000,
>
> ntwx=100,
>
> dt=0.002,
>
> nmropt=1,
>
> ntb=1,
>
> ntp=0,
>
> cut=10.0,
>
> ioutfm=1,
>
> ntxo=2,
>
> /
>
> &wt
>
> type='TEMP0',
>
> istep1=0,
>
> istep2=50000,
>
> value1=0.0,
>
> value2=50.0
This namelist is not terminated.
>
> &wt type='END' /
>
> Hold protein fixed
>
> 10.0
>
> RES 1 509
This may have to go to the very end of the file and is not part of a
namelist.
> /
There is no namelist that this slash would terminate. Namelists cannot
be nested.
> &rst
>
> restraint = "distance( (5716) (6163) )"
>
> restraint = "distance( (1297) (6163) )"
>
> restraint = "distance( (5756) (6163) )"
>
> restraint = "distance( (5348) (6163) )"
>
> restraint = "distance( (5134) (6163) )"
>
> restraint_wt = 50.0
>
> /
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Received on Mon Feb 20 2017 - 07:00:02 PST
