On Aug 9, 2010, at 9:14 AM, Catein Catherine wrote:
>
> Dear Jason,
>
>
>
> This is the method I used?
>
>
>
>>>> 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:
Yes. The basic NCSU framework is available in Amber10, but that does not include
the LCOD addition. You will have to replace the files, EXACTLY AS DESCRIBED IN THE
TUTORIAL, for the LCOD method to be available. You will have to rebuild sander
after the files are replaced. Make a backup of the files before you replace them.
If you feel uncomfortable replacing these files, you can do a linear combination
restraint using the "generalized distance coordinate restraint" (Thanks to Jason Swails
for pointing this out to me). See page 175 (or thereabouts) in the Amber11.pdf file.
I think it is also described on page 170 of the Amber10 manual.
By the way, the tutorial DOES work, you just have to follow the instructions carefully.
Good luck,
Bud Dodson
>>>>
>>>>
>>>>
>>>>
>>> ==============================================================================
>>>>
>>>>
>>>>
>>>> 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
>>>>
>
>
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--
M. L. Dodson
Business email: activesitedynamics-at-comcast-dot-net
Personal email: mldodson-at-comcast-dot-net
Phone: eight_three_two-five_63-386_one
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Received on Mon Aug 09 2010 - 09:00:03 PDT
