This document might help:
http://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/
On Tue, Jul 28, 2020 at 11:49 AM Pinky Mazumder <pmazumder67.gmail.com> wrote:
>
> Hi Lachele,
>
> Still I am having problems with the methyl derivative. Could you please
> share the command of checking derivative charge on the molecule?
>
> Thanks!
>
> On Mon, Apr 20, 2020 at 1:48 AM Lachele Foley <lf.list.gmail.com> wrote:
>
> > What do you mean by "converted"? Do you mean that you added TER cards
> > to the PDB file? Did you do anything else?
> >
> > The way to really check bonding is to generate topology/coordinate
> > files (parm7/rst7) and then load them into a viewer like VMD or
> > Chimera. When I do that, and output a set of pamr7/rst7 files, the
> > bonding looks ok. I don't have xleap at easy access at the moment, so
> > I'm can't check the behavior there, but it's not super important.
> >
> > Note that you will also need to alter the charge on the C atom where
> > the MEX is attached. The website does that automatically where it
> > can, but there is no standard way to encode charge in a PDB file, so
> > if you need to use the PDB file like you are, then you will need to
> > adjust charge. The doc is below.
> >
> >
> > http://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/
> >
> > I used these commands in tleap:
> >
> > source leaprc.GLYCAM_06j-1
> > m = loadpdb hema_TER.pdb ## I added TER cards to the PDB file you
> > sent a couple emails ago
> > check m ## this gets tleap to perform some simple checks on your
> > molecule, including total charge - should be zero if correct
> > saveamberparm m m.parm7 m.rst7
> > quit
> >
> > Then, I loaded them into vmd with:
> >
> > vmd m.parm7 m.rst7
> >
> > Make sure that this works by itself, then try to combine this and your
> > other molecule.
> >
> > I've attached the PDB file with the TER cards added.
> >
> > Let me know if you have other questions.
> >
> > On Mon, Apr 20, 2020 at 1:05 AM Pinky Mazumder <pmazumder67.gmail.com>
> > wrote:
> > >
> > > 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
> >
> >
> >
> > --
> > :-) 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
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed Jul 29 2020 - 00:30:02 PDT
