On Mon, 2014-01-20 at 09:51 +0530, Sushi Shilpa wrote:
> Dear sir,
>
>
> I am simulating 120 amino acids protein in that we have already solved 109
> residues structure, the structure of the last 11 residue is missing, I want
> to hold till 94 while heating, I used input file like this
> Stage 1 heating of 0 to 300K
> &cntrl
>
> imin=0, irest=1,
> ntx=5,
> nstlim=10000,
> dt=0.002,
> ntc=2,
> ntf=2,gsba=1,
This should be "gbsa", not "gsba".
> ntp=0,
> taup=0.2,
> ntt=3,
> gamma_ln=2.0,
> tempi=0.0,
> temp0=300.0,
> ntpr=500,
> ntwx=500,
> ntb=0,
> igb=8,
>
> cut=999.,rgbmax=999.
>
> /
>
> Hold fixed
> 5.0
>
> RES 1
> 94
> END
>
> END
I'm not sure if your input file actually has blank lines between the 5.0
and RES cards (and the last 2 END cards), but I would suggest getting
rid of the blank lines (and the '1' and '94' have to be on the same
line, too). It may work with the blank lines, but I've never tried it
(and I know it works without them).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jan 20 2014 - 04:30:02 PST
