Thanks Lachele!
I initially thought TER card would take up one atom numbering, but it turned
out not, meaning I do not have to renumbering subsequent atoms every time I
add a TER card.
So my oligosaccharide seems to be recognized by GLYCAM_06 ff.
But when I loaded the protein-sugar complex into tleap with GLYCAM_06 ff, it
seems those terminal amino acids were not recognized. I got screen info such
as:
Unknown residue: ASP number: 0 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
-no luck
...
Unknown residue: PRO number: 434 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
...
But every amino acid residue (including terminal ones) had its new residue
created, like
...
Creating new UNIT for residue: PRO sequence: 435
Created a new atom named: N within residue: .R<PRO 435>
Created a new atom named: CA within residue: .R<PRO 435>
Created a new atom named: C within residue: .R<PRO 435>
Created a new atom named: O within residue: .R<PRO 435>
Created a new atom named: CB within residue: .R<PRO 435>
Created a new atom named: CG within residue: .R<PRO 435>
Created a new atom named: CD within residue: .R<PRO 435>
Created a new atom named: OXT within residue: .R<PRO 435>
...
So why there is no hydrogen atoms? Do I need to manually add them? I asked
this because hydrogen atoms on my oligosaccharide were added automatically
with loadpdb command, as
Leap added 57 missing atoms according to residue templates:
57 H / lone pairs
The file contained 3323 atoms not in residue templates
And the total charge is 0 now, which should be +1 according to the protein's
COO and NH3 sidechains (the sugar is neutral).
Could anyone please help me out?
Thank you.
Yun
On Fri, Aug 12, 2011 at 11:28 AM, Lachele Foley (Lists)
<lf.list.gmail.com>wrote:
> Before reordering, I would just insert TER cards between each residue.
> This will instruct leap not to try bonding them. Then, in leap, you
> can use the "bond" command to link the residues together properly.
> Still laborious, but not quite as much.
>
> Sorry... no script.
>
>
> On Fri, Aug 12, 2011 at 1:53 PM, Yun Shi <yunshi09.gmail.com> wrote:
> > 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
> >> >> >
> >> >> _______________________________________________
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> >> >
> >>
> >>
> >>
> >> --
> >> :-) Lachele
> >> Lachele Foley
> >> CCRC/UGA
> >> Athens, GA USA
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Fri Aug 12 2011 - 19:30:03 PDT
