Dear amber users,
I’ve been running SMD for my protein and its ligand in explicit solvent using LCOD.
In order to start the steering at the right value, I’d like to put an “X” as the beginning value of the steering path. In order to see if this feature is still working, I’ve tried first on A10 tutorial and, although I’ve run it several times, I get this odd error message that I didn’t get before (even when I remove the “X” and I try to re-run with a value of 0.7):
** NFE-Error ** : Cannot read &colvar namelist!
I’ve double checked and the cv.in file is in the directory:
sandiego:Athena rhtichau$ ls
cv.in mr_pd-10-500.rst mr_pd-20-10.out smd.txt
mdin mr_pd-10.nc mr_pd-50.nc smd_10-50.txt
mdinfo mr_pd-10.out mr_pd-50.out smd_10-500.txt
mr_pd-10-50.nc mr_pd-10.rst mr_pd-50.rst smd_10.txt
mr_pd-10-50.out mr_pd-100.nc mr_pd.nc smd_100.txt
mr_pd-10-50.rst mr_pd-100.out mr_pd.out smd_50.txt
mr_pd-10-500.nc mr_pd-100.rst mr_pd.rst test_harm-outputfreq
mr_pd-10-500.out mr_pd-20-10.nc qmmm_region.pdb
I guess it’s some very silly mistake and yet I can’t see it. Please help me find it. Following are the input and the cv.in files:
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, infe=1,
/
&qmmm
qmmask=':*',
qmcharge=0,
qm_theory='PM3',
qmshake=0,
writepdb=1,
/
&smd
output_file = 'smd_20-10.txt'
output_freq = 10
cv_file='cv.in'
/
&colvar
cv_type = 'LCOD'
cv_ni=4, cv_i = 8,9,7,9,
cv_nr=2, cv_r = 1.0,-1.0,
npath =2, path = X,-0.7,
nharm=1, harm = 20.0
/
I tried to run the calculation with the following command:
$AMBERHOME/bin/sander -i mdin -p ../../01/mr.top -c ../../01/mr_eq.rst -o mr_pd-20-10.out -r mr_pd-20-10.rst -x mr_pd-20-10.nc
Thanks in advance for any suggestion,
Ruth
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Received on Wed Dec 07 2016 - 05:00:03 PST
