Yes. You can make backups of the existing libraries if you want (copy
to "file.back"). If you diff the files, you should see that the only
significant changes are in the assignment of atom types in the
terminal residues. They were mistakenly assigned in the original
files.
On Sun, Jan 16, 2011 at 12:55 PM, Jianhui Tian <jianhuitian.gmail.com> wrote:
> Sure, thanks. I will try that also. Is it safe to cover the existing file
> with the updated libraries?
>
> JH
>
> On Sun, Jan 16, 2011 at 10:38 AM, Lachele Foley (Lists)
> <lf.list.gmail.com>wrote:
>
>> You can glycosylate a terminal amino acid if that is what you want to
>> do, but you will need the updated libraries. We didn't make a bugfix
>> for that because people very seldom want to do that.
>>
>>
>> On Sun, Jan 16, 2011 at 12:22 PM, Jianhui Tian <jianhuitian.gmail.com>
>> wrote:
>> > Thanks Lachele.
>> > By changing the glycosylation site to a non-terminal amino acid, I
>> produced
>> > the topology file successfully.
>> >
>> > JH
>> >
>> > On Sat, Jan 15, 2011 at 9:44 PM, Lachele Foley (Lists) <
>> lf.list.gmail.com>wrote:
>> >
>> >> The way to fix it depends on your situation. The problem is that you
>> >> have instructed leap to bond atoms together for which it does not have
>> >> sufficient rules. Here are a few guesses.
>> >>
>> >> * If you are loading a pdb file and there is not a TER card between
>> >> the last amino acid and the first glycan residue, then you need one.
>> >> You will have to set the bonding between glycan and protein explicitly
>> >> within leap. The AmberTools manual contains more information.
>> >>
>> >> * If you are trying to attach the glycan to a terminal amino acid,
>> >> then you need to download fresh library files from our site
>> >> (http://glycam.ccrc.uga.edu/ccrc/pages/temp/gl_params.jsp). Just copy
>> >> those over the existing ones in your amber tree or specify their path
>> >> in a customized leap input file.
>> >>
>> >> * It is possible that the amino acid to which the glycan attaches was
>> >> not renamed properly.
>> >>
>> >> * You might be asking leap to bond the glycan to the PDB residue
>> >> number, which might not be the same number assigned internally by
>> >> leap.
>> >>
>> >> * It is also possible that the residue(s) in your glycan are not named
>> >> properly, are in the wrong order, etc.
>> >>
>> >> If none of those is the problem, or if you still need help, then I
>> >> need more info. Did you use our builder (glycam.org/ccrc/gp) to
>> >> generate a pdb to use for input? If not, how did you build the
>> >> glycoprotein? What were the specific commands you issued to leap?
>> >> Which version of Amber? If the Amber is recent enough, which version
>> >> of AmberTools? Did you follow the instructions in the AmberTools
>> >> manual?
>> >>
>> >> :-) Lachele
>> >>
>> >>
>> >> On Sat, Jan 15, 2011 at 10:20 PM, Jianhui Tian <jianhuitian.gmail.com>
>> >> wrote:
>> >> > Hi,
>> >> >
>> >> > I am trying to build the topology for a glycoprotein in Xleap using
>> >> > Glycam_06 and AMBER99SB. When I try to save the topology, it gives
>> >> warning
>> >> > that:
>> >> >
>> >> > Could not find angle parameter: N - CT - HP
>> >> >
>> >> > Can anyone tell me how to solve the problem? Thanks a lot.
>> >> >
>> >> > JH
>> >> > _______________________________________________
>> >> > 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
>> >>
>> > _______________________________________________
>> > 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
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Sun Jan 16 2011 - 10:30:04 PST
