The steps in the tutorial10 use the NCSU codes -- I was talking about the
NMR restraint codes. Also, we need a better description of "doesn't work"
in order to diagnose the problem. What did you do? What step failed? What
was the error message? etc.
All the best,
Jason
On Mon, Aug 9, 2010 at 12:26 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Dear All,
>
>
>
> Thank you Jason's command. I am writing to ask how to run LCOD in AMBER10.
> I follows the description in tutorial A10, it doesn't work. Did I miss
> anything in the following steps (email below)? Did anyone able to run LCOD
> in AMBER10?
>
>
>
> Best regards,
>
>
>
> Cat
>
>
>
> > From: askamber23.hotmail.com
> > To: amber.ambermd.org
> > Date: Fri, 6 Aug 2010 16:11:15 +0800
> > Subject: [AMBER] Error message when doing A10 tutorial (SMD with LCOD)
> with AMBER 10.
> >
> >
> > Dear Sir/Madam,
> >
> >
> >
> > I am using AMBER10. I want to do the SMD analysis as tutorial A10. I
> downloaded all the files from the tutorial.
> >
> >
> >
> > As LCOD reaction coordinate is not available in AMBER10, I also
> downloaded the code in the tutorial and followed the readme file to install
> the LCOD-amber10.tgz file. In the $AMBERHOME/src/sander directory, I type
> "tar xvfz /LCOD-amber10.tgz". In the same directory, I type "make sander".
> In the $AMBERHOME/src/sander directory, I can see a number of related files
> as follows:
> >
> >
> >
> > >>ls *colvar*
> > _ncsu-colvar.f ncsu_colvar.mod _ncsu-colvar-utils.f
> > ncsu-colvar.f ncsu-colvar.o ncsu-colvar-utils.f
> > _ncsu-colvar-math.f _ncsu-colvar-type.f ncsu_colvar_utils.mod
> > ncsu-colvar-math.f ncsu-colvar-type.f ncsu-colvar-utils.o
> > ncsu_colvar_math.mod ncsu_colvar_type.mod
> > ncsu-colvar-math.o ncsu-colvar-type.o
> >
> >
> > Thus, I seems to me that it is installed already. However, when I run the
> same input files I downloaded from the tutorial A10 by typing the following
> command line in console
> >
> >
> >
> > " $AMBERHOME/exe/sander -O -i mdin -o test2.out -p mr.top -c restrt -r
> test2.rst -x test2.mdcrd "
> >
> >
> >
> > Following error message appears in the test2.out file
> >
> >
> >
> >
> ===============================================================================
> >
> > MR
> > begin time read from input coords = 925.000 ps
> >
> > Number of triangulated 3-point waters found: 0
> >
> > Sum of charges from parm topology file = -0.00010000
> > Forcing neutrality...
> >
> > ** NCSU-Error ** : CV type 'LCOD' is not supported so far (CV #1)
> >
> ===============================================================================
> >
> >
> >
> > It seems to me that sander still cannot recognize the LCOD command. Do
> you think I still need to modify the input file below to get it work:
> >
> >
> >
> >
> ==============================================================================
> >
> >
> >
> > Malonaldehyde: NCSU steered MD: LCOD rxn coord
> > &cntrl
> > imin = 0,
> > irest = 1,
> > ntx = 5,
> > ntb = 0,
> > cut = 999.0,
> > tempi = 300.0,
> > temp0 = 300.0,
> > ntt = 3,
> > gamma_ln = 1.0,
> > ntf = 2, ntc = 2, tol = 0.00001,
> > dt = 0.0005,
> > ntpr = 50, ntwr=100, ntwx = 100,
> > nstlim = 100000,
> > ifqnt = 1,
> > /
> > &qmmm
> > qmmask=':*',
> > qmcharge=0,
> > qm_theory='AM1',
> > qmshake=0,
> > writepdb=1,
> > /
> >
> > ncsu_smd
> >
> > output_file = 'smd.txt'
> > output_freq = 1000
> >
> > variable
> > type = LCOD ! Linear Combination of Distance
> > i = (8,9,7,9)
> > r = (1.0,-1.0)
> > path = (0.7,-0.7)
> > harm = (1000.0)
> > end variable
> >
> > end ncsu_smd
> >
> =======================================================================================
> >
> >
> >
> >
> >
> > CAt
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Aug 09 2010 - 06:30:05 PDT
