Dear All,
I have a question about my output.
The input shows below.
But I can get all the ouput files but the -x sa.crd and -e sa.en.
Any suggestion?
By the way, I get an error from the mdinfo file
Ewald error estimate: 0.1000E+01
What do this mean?
Thank you in advance.
MY INPUT:
cat <<eof >sa.in
#
simulated annealing
#
&cntrl
imin=0,nmropt=1,
irest=0,
ntpr=500,
ntb=0, cut=12.0,
nstlim=15000,
ntt=1, tempi=0.0, temp0=300.0, vlimit=20,
&end
#
# Simple simulated annealing algorithm:
#
&wt type='TEMP0', istep1=0,istep2=1000,value1=10.,
&wt type='TEMP0', istep1=0,istep2=1000,value1=10.,
value2=400., &end
&wt type='TEMP0', istep1=1001, istep2=3000, value1=400.,
value2=400.0, &end
&wt type='TEMP0', istep1=3001, istep2=15000, value1=0.,
value2=0.0, &end
#
# Strength of temperature coupling:
#
&wt type='TAUTP', istep1=0,istep2=3000,value1=0.2,
value2=0.2, &end
&wt type='TAUTP', istep1=3001,istep2=11000,value1=4.0,
value2=2.0, &end
&wt type='TAUTP', istep1=11001,istep2=13000,value1=1.0,
value2=1.0, &end
&wt type='TAUTP', istep1=13001,istep2=14000,value1=0.5,
value2=0.5, &end
&wt type='TAUTP', istep1=14001,istep2=15000,value1=0.05,
value2=0.05, &end
#
# "Ramp up" the restraints over the first 3000 steps:
#
&wt type='REST', istep1=0,istep2=3000,value1=0.1,
&wt type='TAUTP', istep1=13001,istep2=14000,value1=0.5,
value2=0.5, &end
&wt type='TAUTP', istep1=14001,istep2=15000,value1=0.05,
value2=0.05, &end
#
# "Ramp up" the restraints over the first 3000 steps:
#
&wt type='REST', istep1=0,istep2=3000,value1=0.1,
value2=1.0, &end
&wt type='REST', istep1=3001,istep2=15000,value1=1.0,
value2=1.0, &end
&wt type='END' &end
LISTOUT=POUT
DISANG=dummy
eof
/sander -O -i sa.in \
-o sa.out \
-p prmtop.sh3 \
-c min1.crd \
-e sa.en \
-r restrt.crd \
-x sa.crd
From prbj_at_rediffmail.com 21 Oct 2002 18:19:40 -0000
Message-id: <20021021181940.8715.qmail.webmail8.rediffmail.com>
Date: 21 Oct 2002 18:19:40 -0000
From: Prem Raj <prbj_at_rediffmail.com>
To: AMBER list <amber.heimdal.compchem.ucsf.edu>
Subject: Re: reg: MAC OS
In-Reply-to: <reg: MAC OS>
Dear Sir,
thanks a lot for the help. I shall try compiling it.
I did not understand the second part. can I run NMR refinement on
RNA systems (using amber) with dipolar coupling constant data.
The NMR tutorial available on the amber site does not discuss any
calculation with dipolar couplings.
at the moment we are running the calculation using Dyana.
we plan to do it on amber.
thanking you
Prem raj
On Mon, 21 Oct 2002 David A. Case wrote :
>On Mon, Oct 21, 2002, Prem Raj wrote:
>
> > I like to know whether there are plans to impliment amber on
>MAC
> > operating system.
>
>We have compiled and tested sander, using g77 (Mac OS X).
>Benchmark results
>(on a pretty old machine) are at the Amber web site.
>
>I would guess (hope) that everything would compile and run in a
>straighforward
>way. You will need an Xserver and X development libraries to run
>xleap.
>
> >
> > secondly I would like to know whether it is possible to run
>NMR
> > refinement (Using amber) on DNA/RNA systems with dipolar
> > couplings.
>
>Yes. We have a manuscript in preparation on this, but nucleic
>acids are
>not fundamentally any different than proteins as far as dipolar
>couplings
>are concerned.
>
>..good luck...dac
>
>--
>
>==================================================================
>David A. Case | e-mail:
>case_at_scripps.edu
>Dept. of Molecular Biology, TPC15 | fax:
>+1-858-784-8896
>The Scripps Research Institute | phone:
>+1-858-784-9768
>10550 N. Torrey Pines Rd. | home page:
>La Jolla CA 92037 USA |
>http://www.scripps.edu/case
>==================================================================
>
Received on Mon Oct 21 2002 - 11:19:17 PDT
