Thanks for your reply, the reason I did the restraints in this way is I was
having trouble using the igr and iat flags in conjunction with each other
to setup a centre of mass restraint (and so followed an example of a
similar setup in archives of the mailing list).
Using the simpler form of the restraints as you suggested if:
C1: 1996
C2: 1998
C3: 1992
C4: 1965
C5: 1962
O5: 1975
and
CD: 544
would a restraint file of :
&rst
r1=-500,r2=3.0,r3=3.0,r4=500,
rk2=100,rk3=100,
iresid=0,
iat=-1,-1,
igr1=1996,1998,1992,1965,1962,1975,igr2=544,
/
do the same thing:
I have just done a quick test and it appears to work but wanted to double
check.
Thanks,
M
On 4 December 2013 02:33, case <case.biomaps.rutgers.edu> wrote:
> On Tue, Dec 03, 2013, Mike Limb wrote:
> >
> > In each of these MD simulations I fix the ligand in position using a COM
> > restraint that is specified in rc.con
> >
> > # COM restraint with NAM-D and CD of Glu35 (between 1 and 6 A)
> >
> > &rst
> > r1=-500,r2=1.0,r3=6.0,r4=500,
> > rk2=50,rk3=50,
> > iresid=1,
> > iat=130,35,
> > ATNAM(1)='C1','C2','C3','C4','C5','O5',
> > ATNAM(2)='CD',
> > /
>
> Try using the simpler form for COM restraints, in which you have iresid=0,
> and use iat<0 to indicate a com group and igr1 to give the atom numbers in
> the
> group.
>
> [Are you sure the above works in sander? You syntax looks wrong: atnam(1)
> is
> supposed to be a four-character string, and you are giving it something
> very
> different.]
>
> ...dac
>
>
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--
Mike Limb
PhD Candidate
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Supervisor: Prof. Adrian Mulholland
Centre for Computational Chemistry
School of Chemistry
University of Bristol
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Received on Wed Dec 04 2013 - 04:00:02 PST
