On Sun, Aug 27, 2017, Parviz Seifpanahi Shabane wrote:
> I need to put a restraint on just part of my proteins during the production
> step. My system is the slice of Nucleosome ( the mixture of DNA and histone
> protein), first I created the PDB file from my topology and coordinate
> files by "ambpdb", from this PDB files I found the residue number which I
> wanted to be free (residue 111 to 134). I tried different methods for
> applying restraint (below), but none of them worked. I checked "mdout" file
> the restrained energy in all of the cases is zero.
Did you set ntr=1 in the cntrl namelist?
The restrainmask syntax is much simpler, e.g.
ntr=1, restraint_wt=10.0, restraintmask=":1-110,135-201",
will restrain all residues in the range 1-201 except for 111-134. You don't
need any group cards here.
...hope this helps....dac
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Received on Sun Aug 27 2017 - 14:00:03 PDT
