I tried to create a rst.dist file by hand and do MD run with it. The file is:
&rst
ixpk= 0, nxpk= 0, iat= 5, 55, 0, 0, r1= 1.30, r2= 1.80, r3= 3.00, r4= 3.50,
rk2=20.0, rk3=20.0, ialtd=0
&end
&rst
iat=0,0,0,0
&end
But when use ambpdb to get the pdb file from this MD run, i found the two
molecules drifted apart, it seems that no restraint applied. So i don't know
what to do.
thanks a lot!
Shuting
Quoting "David A. Case" <case.scripps.edu>:
> On Fri, Jun 10, 2005, gtg549i.mail.gatech.edu wrote:
> >
> > I try to use the "makeDIST_RST", but it give me the following info:
> >
> > > makeDIST_RST -upb 7col.dist -pdb compl_cP3.pdb -rst RST.dist
> > # makeDIST_RST
> > Currently configured for up to 5000 atoms
> > Using MAP file /usr/local/amber8/dat/map.DG-AMBER
> > ERROR no map function for H70 BE2 :data= 1 BE2 H70 2 MAA O6
> > 3.0
> >
> > I guess this is because my residues are not standard residues (BE2 and MAA
> are
> > two organic molecules).
>
> If you have non-standard residues, you will need to input the restraints
> using
> the "raw" restraint format described in the sander section in the manual,
> rather than by using the makeDIST_RST program. The latter program is not
> really designed for non-standard residues.
>
> ...dac
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Received on Fri Jun 10 2005 - 21:53:00 PDT
