Hi,

I have just created a DGlcpAb1-4DGlcpNSa1-4DGlcpAb1-4DGlcpNSa1-4LIdopA[2S]a1-4DGlcpNSa1-4DGlcpAb1-OH   using GAG builder.

However when I try to run tleap on the generated pdb using:

 source leaprc.GLYCAM_06j-1   
 loadamberprep GLYCAM_06j-1.prep
 loadamberprep GlcNS_preliminary.prep
hepc = loadpdb oligo.pdb

I get the following error:

ERROR: Comparing atoms
        .R<0ZB 8>.A<C2 17>, 
        .R<0ZB 8>.A<H1 2>, 
        .R<0ZB 8>.A<O5 3>, and 
        .R<4YS 7>.A<O4 25> 
       to atoms
        .R<0ZB 8>.A<C2 17>, 
        .R<SO3 1>.A<S1 1>, 
        .R<0ZB 8>.A<O5 3>, and 
        .R<4YS 7>.A<O4 25> 
       This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL:    In file [chirality.c], line 142
!FATAL:    Message: Atom named S1 from SO3 did not match !

Any help or tips on what I'm doing wrong?

Thanks