look in the sander output- does sander recognize the restraints? does it
list the correct # of atoms matching the mask? if so, is the restraint
energy non-zero?
are the atoms shifted as a group? meaning even if they are shifted, is it
possible that the best-fit process shifts them back to perfect alignment to
refc? if so, perhaps you want a separate fit mask and rms mask.
check these, it's the important information you need to know what's going
on.
On Tue, Dec 16, 2008 at 7:05 PM, Dirar Homouz <dirar.hotmail.com> wrote:
> Dear Amber users,
>
> I'm trying to pull a certain structure using restraintmask from an initial structure
> defined by the input file "inpcrd" to a final structure defined by reference file
> "refc".
> 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.
>
> The code runs fine. However, it doesn't move the structure to the
> coordinates defined by the refc file. I'm not sure why is the refc file
> is not recognized?
>
>
> -Dirar
>
>
>
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Received on Wed Dec 17 2008 - 01:23:06 PST
