Others might comment but I think your mask should be something like
':2276-2299' instead of '.2276-2299'
Also, your restraints are very tight. Is that what you really want to
do? I am running simulations (steered MD) and I put a restraint using
something like 5kcal/molA**2, which is usually enough in my case!
hope this helps,
--alessandro
On Thu, Dec 11, 2008 at 6:30 PM, Dirar Homouz <dirar.hotmail.com> wrote:
> Dear amber users,
>
> I'm trying to pull a certain structure using restraintmask with a specified
> reference file.
> I'm using the following input file
>
> ************************************************************
> &cntrl
> imin = 0, ntb = 0,
> igb = 0, ntpr = 100, ntwx = 100,
> ntt = 3, gamma_ln = 1.0,
> tempi = 300.0, temp0 = 300.0
> nstlim = 100000, dt = 0.001,
> cut = 12.0
> ntr=1,
> ntrx=1,
> restraint_wt=100.0,
> restraintmask='.2276-2299',
> /
> ************************************************************
> with the following command
>
> $AMBERHOME/exe/sander -O -i pull.in -o pull.out -c inpcrd -p prmtop -r
> rst -ref refc
>
>
> The inpcrd file is different from the refc file. The last 24 atoms are
> shifted from their
> initial positions.
>
>
> When I run this simulation, it looks like my structure is being pulled to
> the coordinates in
> the inpcrd file and that the refc coordinates are ignored.
>
> Do you have any idea about what is going on?
>
> Best,
>
> Dirar
>
>
> ________________________________
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> now.
--
[ ]s
--alessandro
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Received on Fri Dec 12 2008 - 01:20:03 PST
