Hi Elvis,

*"However, there is an additional OH attached to C2 which has no names." *I
assume you mean that in the 3D structure there is a reducing terminal
oxygen, and you don't know what to name it in the PDB file? The oxygen
should be named O1, the hydrogen HO1 and the residue as ROH.

If you build DNeup5Aca2-OH on <> you
can check the PDB file for what GLYCAM requires. The reducing terminal
section looks like this:
HETATM    1  HO1 ROH     1       5.998   8.375  -1.724  1.00  0.00
HETATM    2  O1  ROH     1       6.265   8.935  -2.457  1.00  0.00
HETATM    3  C2  0SA     2       7.667   9.136  -2.407  1.00  0.00
HETATM    4  C1  0SA     2       7.999   9.869  -1.055  1.00  0.00
... etc

As long as the carbohydrate is linear (not branched) and you have the
residues correctly named and in the appropriate order, there is no need to
explicitly "link" them in tleap. Tleap will automatically bond sequential
residues as it does for amino acids in proteins. If you had a branched
carbohydrate, then you would insert TER cards at the branch points and use
the "bond" command in tleap.


On Fri, May 27, 2016 at 9:20 AM, Elvis Martis <[log in to unmask]>

> Hello,
> I am trying to simulate N8-neuraminidase bound to sialic acid in AMBER14.
> In order to use GLYCAM_06j-1 paramters for sialic acid, I edited
> everything necessary. For example, residue name was changed to "0SA" and
> then the atom names were changed as per the atom names in "0SA". However,
> there is an additional OH attached to C2 which has no names. As per Prof.
> Case's suggestion in "AMBER Digest, Vol 1588, Issue 1:message 5" we must
> link "0SA" to "ROH",  this I am not clear how to do it.
> Can someone help me here?
> Thanks in Advance.
> Regards
> Elvis Martis