When you copy the chains, they have exactly the same x,y,z
coordinates. In other words, they are right on top of each other.
You will need to use the translate and/or transpose commands to put
them into the proper relative geometries.
On Fri, May 15, 2020 at 11:53 PM Pinky Mazumder <pmazumder67.gmail.com> wrote:
>
> Please discard my previous message.
>
>
> Thank you so much for your cordial response.
>
>
> I can copy the chain using this command and the numbers of atoms are
> increasing.
>
>
> However, I am not able to see the two chains together in vmd or in the
> xleap using the edit command.
>
>
> Could you please help me in this regard?
>
>
> Thank you again.
>
> Sincerely,
> Pinky
>
> On Fri, May 15, 2020 at 10:51 PM Pinky Mazumder <pmazumder67.gmail.com>
> wrote:
>
> > Thank you so much for your cordial response.
> >
> >
> > But, I can show the two chains together using vmd. I can copying the chain
> > because the numbers of atoms are increasing.
> >
> >
> > However, I am not able to see the two chains together.
> >
> >
> > Could you please help me in this regard?
> >
> >
> > Thank you again.
> >
> > Sincerely,
> >
> > On Fri, May 15, 2020 at 10:09 PM Lachele Foley <lf.list.gmail.com> wrote:
> >
> >> First, you need to know the geometric relationships between the
> >> chains. The relationships will differ based on the source of the
> >> cellulose.
> >>
> >> In leap, you can use:
> >>
> >> chain2 = copy chain1
> >>
> >> to make a copy of a chain.
> >>
> >> Then, once you know the relative geometries, you can use translate
> >> and/or transform to position the chains properly with respect to each
> >> other.
> >>
> >> Alternatively, find an experimentally-determined structure, such as an
> >> X-ray or cryo-EM structure.
> >>
> >> Also consider contacting Dr. Jodi Hadden. She can probably help you,
> >> but she's pretty busy with other stuff, so you might have to be
> >> patient.
> >>
> >> On Fri, May 15, 2020 at 1:01 PM Pinky Mazumder <pmazumder67.gmail.com>
> >> wrote:
> >> >
> >> > Hi David,
> >> >
> >> >
> >> > Thank you for your response.
> >> >
> >> >
> >> >
> >> > I have been able to make the polymer of cellulose. But I need multiple
> >> > chains together.
> >> >
> >> >
> >> > Could you please suggest how can I replicate the same polymer chain or
> >> can
> >> > I build the multiple number of polymer chain together?
> >> >
> >> >
> >> > Is there any specific tutorial or command that I need to follow?
> >> >
> >> >
> >> > Thank you.
> >> >
> >> >
> >> > Kind regards,
> >> >
> >> > Pinky
> >> >
> >> > On Sun, Apr 5, 2020, 12:20 PM David A Case <david.case.rutgers.edu>
> >> wrote:
> >> >
> >> > > On Thu, Apr 02, 2020, Pinky Mazumder wrote:
> >> > > >
> >> > > >I want to build a chain of cellulose. So when I am trying to do this
> >> by
> >> > > >using foo sequence command.
> >> > > >
> >> > > > It says that '' Error : sequence : ILLEGAL UNIT named Glc''.
> >> > >
> >> > > Are you inside tleap at this point? If so, execute the "list"
> >> command,
> >> > > and see if Glc is one of the units listed. If not, you would need to
> >> > > somehow load the units you want.
> >> > >
> >> > > Carbohydrates are discussed in Chap. 3 of the Amber Reference Manual:
> >> > > you might see if that would help.
> >> > >
> >> > > If this is not a tleap error, then please give more details about
> >> > > exactly what you mean by "using foo sequence command".
> >> > >
> >> > > ...thx...dac
> >> > >
> >> > >
> >> > > _______________________________________________
> >> > > AMBER mailing list
> >> > > AMBER.ambermd.org
> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> :-) Lachele
> >> Lachele Foley
> >> CCRC/UGA
> >> Athens, GA USA
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> > --
> > Pinky, Sharmi
> > AL,US
> >
>
>
> --
> Pinky, Sharmi
> AL,US
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Sat May 16 2020 - 03:00:02 PDT
