Dear Amber Developers:
I'm trying to use the ncsu_smd codes for steered MD. Basically I want to steer two Glcnac rings to their positions in a known crystal structure. Below is my MD input file:
MD production run at NPT
# control section
&cntrl
irest = 1,
ntx = 5, ntb = 2, ntp = 1,ntwprt=4675
cut = 8.0, ntt = 3, gamma_ln = 2,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0, tautp = 2.0,
nstlim = 100000000, dt = 0.002,
ntpr = 30000, ntwx = 10000, ntwv = 0, ntwe = 0,
nmropt = 0, ntr=1, ioutfm =1,iwrap=1,ig = -1,
/
Restrain all backbone CA atoms
10.0
ATOM 5 5
...... ...... ......
...... ...... ......
ATOM 4367 4367
/
ncsu_smd
output_file = 'xx_smd.txt'
output_freq = 10000
variable
type= MULTI_RMSD
i=(4618, 4636, 4632, 4628, 4621, 4620, 0, 4646, 4664, 4660, 4656, 4649, 4648, 0)
r=(47.228, 38.993, 29.383,
48.172, 39.346, 30.539,
47.472, 40.312, 31,486,
47.010, 41.547, 30.733,
46.155, 41.145, 29.525,
46.917, 40.161, 28.700,
46.955, 30.894, 40.394,
47.928, 31.919, 41.011,
49.322, 31.437, 40.654,
49.559, 30.004, 41.103,
48.484, 29.062, 40.595,
47.239, 29.616, 40.816)
path = (X,0) path_mode = LINES
harm = (10.0)
end variable
end ncsu_smd
END
END
The atom id of the Glcnac rings are defined in "i=" session, and the target coordinates are defined in "r=" session. By submitting a pmemd job with this input file I got the following error:
5. REFERENCE ATOM COORDINATES
default_name
----- READING GROUP 1; TITLE:
ncsu_smd
rfree: Error decoding variable 1 3 from:
output_file
I know update 9 has to be applied for compatibility between ncsu_smd codes and pmemd, and I believe I've done that. Then, my MD input file must be wrong. My rationale for this MD input file come from Amber manual 16, page 434, figure 22.7.
Could somebody help me figure out the issues? Thanks in advance.
Best,
Yao Xiao
Research Assistant
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA
yx55537.uga.edu
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Received on Mon Jul 24 2017 - 14:00:03 PDT
