On Tue, Jul 1, 2014 at 8:31 AM, Asmita Gupta <asmita4des.gmail.com> wrote:
> Dear users,
>
>
> I am trying to set up an SMD run using this input file (the ncsu_smd
> section has been taken from the amber tutorial files)
>
> &cntrl
> imin = 0,
> irest = 1,
> ntx = 5,
> ntb = 2,
> pres0 = 1,
> ntp = 1,
> taup = 2.0,
> cut = 10.0,
> ntc = 2,
> ntf = 2,
> tempi = 300.0,
> temp0 = 300.0,
> ntt = 3,
> ig = -1,
> ioutfm = 1,
> iwrap = 1,
> gamma_ln = 1.0,
> nstlim = 100000, dt = 0.0005, tol = 0.00001,
> ntpr = 500, ntwx = 500, ntwr = 5000000
> /
> ncsu_smd
> output_file = 'smd.txt'
> output_freq = 1000
>
> variable
> type = LCOD
> i = (8,9,493,494)
> r = (1.0,-1.0)
> path = (17.5,50)
> harm = (100.0)
> end variable
> end ncsu_smd
>
> =====================
>
> but i am getting this error
>
> "Could not find cntrl namelist"
> =============================
>
> I did a google search for this error and found that this might be due to
> certain formatting issues in mdin file.
>
> But i can't see any formatting error in the mdin file. Can you pls suggest
> what's wrong in this file?
>
&cntrl cannot be on the first line of your input file when you are using
sander. The first line is read as a title and ignored (this is not true
with pmemd as far as I can tell).
I tested an otherwise valid mdin file setting the &cntrl tag on the first
line and I got the same error you did.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 01 2014 - 09:00:04 PDT
