Dear Dan,
Unfortunately, I've tried with a comma after it but I'm still getting the same error message.. I've also added commas in the &smd section but I'm getting the same.
Thank you anyway for your suggestion.
Sincerely,
Ruth
On Wednesday, December 07, 2016 16:07 CET, Daniel Roe <daniel.r.roe.gmail.com> wrote:
Hi,
Seems like you might be missing a comma after
cv_type = 'LCOD'
in the colvar namelist.
-Dan
On Wed, Dec 7, 2016 at 7:32 AM, Ruth Helena Tichauer <rhtichau.laas.fr> wrote:
> 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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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Dec 07 2016 - 10:30:03 PST
