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
>>
> _______________________________________________
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> 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 - 10:00:04 PST
