Thanks a lot Lachele!
You are right that the ordering of my molecule is reverse. But changing the
ordering manually seems to be laborious, do you have a script to do this
kind of thing as there are also CONECT records in the pdb file?
Anyways, I will try changing the order manually first.
Yun
On Fri, Aug 12, 2011 at 10:29 AM, Lachele Foley (Lists)
<lf.list.gmail.com>wrote:
> The ordering of the atoms shouldn't matter. The ordering of the
> residues can make a huge difference.
>
> For example, if you have DGlcpa1-4DManpA1-OH, the three residues are,
> in the order of that string, "0GA", "4MA" and "ROH". However, in the
> pdb file, they need to be ordered ROH first, then 4MA and 0GA.
>
> If the ordering is wrong, you can get around it by inserting TER cards
> between all the residues and setting the bonding explicitly in tleap.
>
> If that still doesn't help, send me your pdb file (you don't have to
> send to the list), and I'll help.
>
> :-) Lachele
>
>
> On Fri, Aug 12, 2011 at 1:19 PM, Yun Shi <yunshi09.gmail.com> wrote:
> > Thank you for the reply.
> >
> > But I want to keep the coordinates as in the original pdb file, and I do
> > notice that the ordering of atoms in my pdb file are different from
> GLYCAM
> > convention.
> >
> > So could anyone suggest a way to format my oligosaccharide in accordance
> > with GLYCAM06 while retaining the coordinates (structure) of my original
> pdb
> > file?
> >
> > Thanks,
> >
> > Yun
> >
> >
> > On Fri, Aug 12, 2011 at 10:00 AM, Oliver Grant <olivercgrant.gmail.com
> >wrote:
> >
> >> Hi,
> >>
> >> Not sure what the problem is without looking at your pdb input file. I
> >> suggest going to glycamweb and building your oligosaccharide and
> comparing
> >> that to what you have.
> >>
> >> Oliver
> >>
> >> On 12 August 2011 04:42, Yun Shi <yunshi09.gmail.com> wrote:
> >>
> >> > Hi All,
> >> >
> >> > Sorry for this lower-level question, but I searched the archive and
> still
> >> > did not solve it.
> >> >
> >> > So I was trying to load a pdb file (only one oligosaccharide molecule)
> >> > after
> >> > source leaprc.GLYCAM_06, but what I got was
> >> >
> >> > ERROR: Comparing atoms
> >> > .R<0hA 1>.A<C3 14>,
> >> > .R<0hA 1>.A<C1 1>,
> >> > .R<0hA 1>.A<H2 19>, and
> >> > .R<0hA 1>.A<O2 20>
> >> > to atoms
> >> > .R<0hA 1>.A<C3 14>,
> >> > .R<2hA 1>.A<C1 1>,
> >> > .R<0hA 1>.A<H2 19>, and
> >> > .R<0hA 1>.A<C1 1>
> >> > This error may be due to faulty Connection atoms.
> >> > !FATAL ERROR----------------------------------------
> >> > !FATAL: In file [chirality.c], line 140
> >> > !FATAL: Message: Atom named C1 from 2hA did not match !
> >> > !
> >> > !ABORTING.
> >> >
> >> > So what it really means by "faulty Connection atoms"? I have already
> >> > changed
> >> > the sugar names according to GLYCAM naming convention.
> >> >
> >> > Any help is appreciated!
> >> >
> >> > Yun
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> _______________________________________________
> >> AMBER mailing list
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> >>
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> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Fri Aug 12 2011 - 11:00:03 PDT
