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
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> 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
Received on Fri Aug 12 2011 - 10:30:05 PDT
