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
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- application/x-aportisdoc attachment: hema.pdb
- application/x-aportisdoc attachment: cell.pdb
Received on Fri Apr 17 2020 - 01:30:01 PDT
