Thank you.
I can place the chains parallel to each other. After that, I need to see
the h-bond interaction between the polymers. For that I ran the simulations
with energy minimization, heating and production MD.
Even after, I do not see the H-Bond. To do so, what process I need to
follow?
Thank you.
Sincerely,
Pinky
On Sat, May 16, 2020 at 4:33 AM Lachele Foley <lf.list.gmail.com> wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Pinky, Sharmi
AL,US
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 29 2020 - 08:00:01 PDT
