AMBER Archive (2005)

Subject: Re: AMBER: rotating and repositioning molecules in xleap

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Sun May 22 2005 - 10:36:16 CDT

If you select the molecule you want to rotate with respect
to another, I believe you can hold down the Ctl and/or Shift
key to rotate. There may be something in 'help edit' about
such commands.

Bill

> Thanks for your reply, but I still have a question.
> I knew that I can rotate molecules in the edit window, but it does not
> modify coordinates of molecules. I mean that I can visually rotate
> molecules in edit window, but when I close the edit, they still have
> original coordinates. I know that I can set up center of box in xleap,
> but I don't know how to modify coordinates by rotating molecules
> conveniently in xleap.
> Thanks for your help in advance.
>
> best,
> Hwankyu.
>
>
> On May 22, 2005, at 5:37 AM, Angelo Pugliese wrote:
>
> > In the Edit window of Xleap there are all the commands that you
> > need....just play around with it.
> >
> > When you connect two molecule they become one single entity ( one
> > molecule) so you need to add parameters for this new molecule....the
> > easiest thing is to find the new parameters by analogy with other
> > parameters already in the AMBER database and upgrade your .frcmod file.
> >
> > Hope it helps
> >
> > Angelo
> >
> >
> >
> > Hwankyu Lee wrote:
> >
> >> Dear Amber-users,
> >>
> >> 1) I'm connecting two molecules in xleap, and want to position those
> >> molecules with specific configuration. I thought I can do that in edit
> >> of xleap, but cannot find how to do this. Could you tell me how to
> >> rotate and reposition molecules in xleap ? Is it possible in edit
> >> (visual tool) of xleap?
> >>
> >> 2) Although I had .frcmod file by using parmchk, when I connected two
> >> molecules, I got an error like "could not find angle parameter" or
> >> "Could not find bond~~". In that case, how can I get reasonable
> >> angle,
> >> bond or torsion parameters?
> >>
> >> Thanks for your help in advance.
> >>
> >> best,
> >> Hwankyu.
> >>
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