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
>> >> > _______________________________________________
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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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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Fri Aug 12 2011 - 11:30:04 PDT
