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
>
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Received on Sun Aug 08 2010 - 21:30:03 PDT
