Francesco Pietra wrote:
> With Amber9 I am applying the scripts of web Tutorial 1B (polyA-polyT) to
> another case. While the tutorial run OK, and the new case also run OK
up to
> section 4, relaxing structure before MD, the MD itself, with command
line:
>
> $AMBERHOME/exe/sander -O -i eqaeqb_gb_md1_12Acut.in -o
eqaeqb_gb_md1_12Acut.out
> -c eqaeqb_gb_init_min.rst -p eqaeqb.prmtop -r eqaeqb_gb_md1_12Acut.rst -x
> eqaeqb_gb_md1_12Acut.mdcrd
>
>
> did not run, tail -f telling:
>
> "Could not find cntrl namelist"
>
> File "eqaeqb_gb_md1_12Acut.in" reads:
>
> # eqaeqb MD Generalised Born, 12 angstrom cut off
> &cntrl
> imin = 0, ntb = 0,
> igb = 1, ntpr = 100, ntwx = 100,
> ntt = 3, gamma_ln = 1.0,
> tempi = 300.0, temp0 = 300.0
> nstlim = 100000, dt = 0.001,
> cut = 12.0
> /
> -------------
>
> A google search did not clarify the problem. As a newcomer to MD I
apologize
> for posting trivial questions, if this is the case.
> Thanks
>
> francesco pietra
>
>
One of the most common cause of this kind of problem seems to be
formatting problems. Be sure there is no blank line before the
one starting with '#'. Also, all entries in the namelist list
should be separated from the rest by a comma. I notice temp0 does
not conform. I'm unclear about the last line: cut = 12.0, but I
always end the last line with a comma as well. The error message
seems to indicate a slightly different problem, but check these
items and try again. Be sure you cut and paste when sending files
or parts of files to the list.
Bud Dodson
--
M. L. Dodson
Email: mldodson-at-houston-dot-rr-dot-com
Phone: eight_three_two-56_three-386_one
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Received on Wed Jul 11 2007 - 06:07:30 PDT
