Hey There GLYCAM,

I'm trying to solvate and add counterions to a HS hexasaccharide in tLEAP. I have built the hexasaccharide using the GLYCAM web server, but once I load the PDB into LEAP, it does not recognize the UYS (GlcNS residue). I know that you released a prep file for GlcNS residues, and I downloaded that and tried loading that in as well, and got the same issue. Did I not format the prep file correctly or am I missing something more?

I've isolated the residue I needed from the prep file, and it looks like this:

UYS INT 0
CORRECT OMIT DU BEG
-0.1940 
1 DUMM DU M 0 -1 -2 0.000 0.000 0.00 0.0000 
2 DUMM DU M 1 0 -1 0.500 0.000 0.00 0.0000 
3 DUMM DU M 2 1 0 1.296 74.264 0.00 0.0000 
4 C1 Cg M 3 2 1 23.519 98.653 -135.65 0.4680 
5 H1 H2 E 4 3 2 1.090 141.692 162.29 0.0000 
6 C2 Cg M 4 3 2 1.558 103.961 13.89 0.2450 
7 H2 H1 E 6 4 3 1.092 106.853 -149.41 0.0000 
8 N2 Ng B 6 4 3 1.486 111.224 93.53 -0.6430 
9 H2N H E 8 6 4 1.009 115.982 -30.97 0.2360 
10 S1 S 3 3 2 1 1.884 119.491 -167.81 1.2450 
11 O1S O2 E 4 3 2 1.446 106.410 -102.07 -0.6940 
12 O2S O2 E 4 3 2 1.437 128.086 115.25 -0.6940 
13 O3S O2 E 4 3 2 1.446 70.631 7.86 -0.6940 
14 C3 Cg M 6 4 3 1.547 112.034 -31.73 0.1650 
15 H3 H1 E 16 6 4 1.092 108.717 70.25 0.0000 
16 O3 Oh S 16 6 4 1.457 109.988 -171.07 -0.6300 
17 H3O Ho E 18 16 6 0.977 109.893 -12.80 0.4130 
18 C4 Cg M 16 6 4 1.546 112.211 -50.71 0.3220 
19 H4 H1 E 20 16 6 1.091 108.977 -70.26 0.0000 
20 C5 Cg 3 20 16 6 1.544 112.523 51.74 0.2460 
21 H5 H1 E 22 20 16 1.092 108.088 68.11 0.0000 
22 C6 Cg 3 22 20 16 1.544 112.817 -173.43 0.3280 
23 H62 H1 E 24 22 20 1.090 110.073 -62.63 0.0000 
24 H61 H1 E 24 22 20 1.090 109.603 179.01 0.0000 
25 O6 Os E 24 22 20 1.444 111.701 58.39 -0.4610 
26 O5 Os E 22 20 16 1.500 111.305 -49.14 -0.5680 
27 O4 Os M 20 16 6 1.448 107.905 171.55 -0.4780 

LOOP 
O5 C1 

DONE 
STOP

Now, I type these commands in leap:

>source leaprc.GLYCAM_06j-1
>loadamberprep UYS.prep
 
Then I get the error message:
** LOOP atom C1 not found - bond not formed
Discarding residue (-0.1940 ) to EOF

Then if I try to load in the PDB of the hexa:

>carb = loadpdb [structure.pdb]

It says that the UYS residues are unrecognized.

Any idea what's going on here?

Thanks,

Sam