Ok, then check the atom names you have assigned to the CH3,
they should be C6, H61, H62, H63 as per GLYCAM_06j-1 for the ZhA.
so your residue entry should somewhat look like this in your input
coordinate file, I guess it is PDB
ATOM <ATOM_NUM> C6 ZhA <RES_NUM> X Y Z .......
ATOM <ATOM_NUM> H61 ZhA <RES_NUM> X Y Z .......
ATOM <ATOM_NUM> H62 ZhA <RES_NUM> X Y Z .......
ATOM <ATOM_NUM> H63 ZhA <RES_NUM> X Y Z .......
X Y Z - being your coordinates
After making this change, then load it in xleap.
Regards
*Elvis Martis* PhD Student, Bombay College of Pharmacy
[image: photo] Email: elvis_bcp.elvismartis.in <elvis_bcp.elvismartis.in>
Website: http://www.elvismartis.in <http://www.elvismartis.in/>
group website: http://www.profeccoutinho.net.in/
Address: Kalina, Santa Cruz [E]
Alt. e-mail: elvis.martis.bcp.edu.in
<
https://in.linkedin.com/in/elvisadrianmartis>
Encrypted E-mail: elvismartis.protonmail.ch
On 21 October 2016 at 20:27, Imma Speciale <i.spec88.gmail.com> wrote:
> [image: Boxbe] <https://www.boxbe.com/overview> This message is eligible
> for Automatic Cleanup! (i.spec88.gmail.com) Add cleanup rule
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>
> The residue name is correct.
>
> I have a ZhA: alpha-L-Rha 2,3OMe.
>
> 2016-10-21 16:42 GMT+02:00 Elvis Martis <elvis_bcp.elvismartis.in>:
>
> > Hi,
> > Please check the residue name for your structure, and check the
> equivalent
> > name in the GLYCAM atom name list.
> > For example, for residue name "4GA" check the legal atom names.
> >
> > Regards
> >
> > *Elvis Martis* PhD Student, Bombay College of Pharmacy
> > [image: photo] Email: elvis_bcp.elvismartis.in <elvis_bcp.elvismartis.in
> >
> > Website: http://www.elvismartis.in <http://www.elvismartis.in/>
> > group website: http://www.profeccoutinho.net.in/
> > Address: Kalina, Santa Cruz [E]
> > Alt. e-mail: elvis.martis.bcp.edu.in
> > <https://in.linkedin.com/in/elvisadrianmartis>
> > Encrypted E-mail: elvismartis.protonmail.ch
> >
> >
> > On 21 October 2016 at 19:56, Imma Speciale <i.spec88.gmail.com> wrote:
> >
> > > Dear all,
> > >
> > > I have builded an olygosaccharide with GLYCAM-Web in order to open it
> > with
> > > Xleap, because this program generates a file pdb that Xleap usually
> open.
> > > In my case, this is not true.
> > >
> > > I have added in the file pdb the flag TER, to indicate the branching
> and
> > I
> > > have opened it in Xleap after loading *leaprc.GLYCAM_06h*, but the
> > program
> > > closes abnormally and in the terminal results the following message:
> > >
> > > ------------------------------------------------------------
> > > ---------------------------------------------------------------------
> > >
> > > !FATAL ERROR----------------------------------------
> > >
> > > !FATAL: In file [chirality.c], line 142
> > >
> > > !FATAL: Message: Atom named CH3 from MEX did not match !
> > >
> > > !
> > >
> > > !ABORTING.
> > >
> > > ------------------------------------------------------------
> > > --------------------------------------------------------------------
> > >
> > > Thus I have loaded another library *leaprc.**GLYCAM_06j-1 *(the same
> > > library used by GLYCAM-WEB to generate the oligosaccharide), but the
> > result
> > > is the same!!
> > >
> > > Xleap doesn't recognize the flag MEX.
> > >
> > > Does anyone know how to fix this?
> > >
> > > Thank you
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Oct 21 2016 - 08:30:03 PDT
