dear sir,
First we creat 10 disaccharide in xleap using GLYCAM_06 force field.
then we
>solvatebox 10_disa SPCBOX 3.0
This is not a cubic box .
to make cubic box we set..
> set 10_disa box {32.0 32.0 32.0}
> saveamberparm 10_disa xxx.prmtop xxx.inpcrd
is it creat cubic box.
then i minimize the system *min.in
*&cntrl
imin=1,
maxcyc=2500,
ncyc=1000,
ntb=1,
ntr=0,
cut=12
/
During minimization by sander * segmentation fault* is coming out.
where is error...? kindly help me.
thanking you
subrata
On Tue, Sep 28, 2010 at 3:52 PM, case <case.biomaps.rutgers.edu> wrote:
> On Tue, Sep 28, 2010, subrata paul wrote:
> >
> > I am simulating 10 disaccharide and 1000 (aprx) SPC/E water molecules.
> after
> > solvating i made cubic box
> > >set *mixer* box { 32.0 32.0 32.0}
>
> Sorry: we still need information about what you really did. What do you
> mean
> by "after solvating"? If you used "solvateBox", then the box information
> is
> already associated with the system. But we need the *full* set of commands
> in
> order to provide any help.
>
> ....dac
>
>
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Received on Tue Sep 28 2010 - 06:30:05 PDT
