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 Fri Aug 06 2010 - 01:30:03 PDT
