Date: Mon, 20 Apr 2020 20:30:07 -0500
Hi Lachele,
I have converted the pdb files using the following command:
*pdb4amber -i orig.pdb -o new.pdb --reduce --dry*
However, I have loaded the pdb files in xleap which is edited by you and
have checked that if the total charge are zero or not. I found that the *unit
hema_TER.pdb is not zero.*
Attached is the screenshot of this. Please find this.
How do I solve this?
Sincerely,
Pinky
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
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(image/png attachment: check_hema.PNG)
