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
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Received on Mon Apr 20 2020 - 00:00:01 PDT
