Date: Mon, 20 Apr 2020 00:05:17 -0500
Hi Lachele,
Hope you are doing well.
I am facing another problem. I have build the hemicellulose chain using
glycam carbo builder. so, for loading it in xleap, it needed to be
converted.
The converted pdb looks fine in vmd. However, when I have loaded it into
xleap, I found that the alpha-glucoronic residue have detached from the
beta-xylose chains.
Attached is the image of vmd as well as xleap. Could you please tell me why
this is happening?
Thank you.
Sincerely,
pinky
On Sat, Apr 18, 2020 at 2:21 AM Lachele Foley <lf.list.gmail.com> wrote:
> Sorry I didn't reply before now. Did you figure it out? Do you still
> need help?
>
> On Fri, Apr 17, 2020 at 5:28 PM Pinky Mazumder <pmazumder67.gmail.com>
> wrote:
> >
> > Hi Lachele,
> >
> > As you said about the combine command. It works.
> >
> > Thank you so much.
> >
> > Sincerely,
> > Pinky
> >
> > On Fri, Apr 17, 2020 at 9:59 AM Pinky Mazumder <pmazumder67.gmail.com>
> wrote:
> >>
> >> Also I do not have the Amber style pdb file. Do I need this for
> combining the two pdb?
> >>
> >> Thank you.
> >>
> >> Sincerely,
> >> Pinky
> >>
> >> On Fri, Apr 17, 2020 at 2:45 AM Pinky Mazumder <pmazumder67.gmail.com>
> wrote:
> >>>
> >>> Thank you for your cordial response.
> >>>
> >>> Here I have attached the two pdb files of cellulose and hemicellulose.
> >>>
> >>> I need to combine those chain as a single pdb so that I can run the
> relaxation.
> >>>
> >>>
> >>> Thank you again.
> >>>
> >>> Sincerely,
> >>> Pinky
> >>>
> >>> On Fri, Apr 17, 2020 at 1:06 AM Lachele Foley <lf.list.gmail.com>
> wrote:
> >>>>
> >>>> That usually means you have a bonding issue. You will often need to
> >>>> make little edits to your PDB file and/or leap commands to get carbs
> >>>> to be loaded properly.
> >>>>
> >>>> Did you download the amber-style pdb file? Can you send me your pdb
> file?
> >>>>
> >>>> On Fri, Apr 17, 2020 at 1:59 AM Pinky Mazumder <pmazumder67.gmail.com>
> wrote:
> >>>> >
> >>>> > Hi Lachele,
> >>>> >
> >>>> > Thank you for your reply.
> >>>> >
> >>>> >
> >>>> > I have build the hemicellulose using glycam carbohydrate builder
> and then I
> >>>> > am trying to load the pdb file of ''hemicellulose'' using loadpdb
> command
> >>>> > in xleap.
> >>>> >
> >>>> > But, It shows the error !FATAL: Message: Atom named C1 from 4LA
> did not
> >>>> > match !
> >>>> >
> >>>> > Attached is the screenshot.
> >>>> >
> >>>> > Do you have any idea why this is happening?
> >>>> >
> >>>> > Any help would be appreciated.
> >>>> >
> >>>> >
> >>>> > Thank you again.
> >>>> >
> >>>> >
> >>>> > Sincerely,
> >>>> > Pinky
> >>>> >
> >>>> > On Thu, Apr 16, 2020 at 3:23 AM Lachele Foley <lf.list.gmail.com>
> wrote:
> >>>> >
> >>>> > > I usually use tleap rather than xleap, but you should be able to
> use
> >>>> > > either. See my previous reply, but also consider the 'combine'
> >>>> > > command.
> >>>> > >
> >>>> > > Learning to use xleap or tleap takes a little time, but the Amber
> >>>> > > manual does a pretty good job of describing the functions.
> >>>> > >
> >>>> > > On Wed, Apr 15, 2020 at 11:14 PM Pinky Mazumder <
> pmazumder67.gmail.com>
> >>>> > > wrote:
> >>>> > > >
> >>>> > > > Dear Amber Users,
> >>>> > > >
> >>>> > > > I have built cellulose chain using xleap command. On the other
> hand,
> >>>> > > > I have made the chain of hemicellulose using GLYCAM_06
> carbohydrate
> >>>> > > builder.
> >>>> > > >
> >>>> > > > Now, I need to put the chain close together.
> >>>> > > >
> >>>> > > >
> >>>> > > > So, my question is, how can I make the both chains closer
> together?
> >>>> > > Should
> >>>> > > > I load the chain of hemicellulose in xleap? If it is, then what
> is the
> >>>> > > > command for this job?
> >>>> > > >
> >>>> > > >
> >>>> > > > Any help would be appreciated. Please forgive me if I am asking
> something
> >>>> > > > silly.
> >>>> > > >
> >>>> > > > Thank you.
> >>>> > > >
> >>>> > > > --
> >>>> > > > Pinky
> >>>> > > > 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
> >>>> > 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
> >>> AL,US
> >>
> >>
> >>
> >> --
> >> Pinky, Sharmi
> >> AL,US
> >
> >
> >
> > --
> > Pinky, Sharmi
> > AL,US
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
-- Pinky, Sharmi AL,US
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(image/png attachment: after_loaded_it_xleap.PNG)
(image/png attachment: converted_hemi_vmd.PNG)
