Hi,

I'm having trouble reading a pdb generated by glycam. I created using heparin/HS builder

DGlcpNSa1-4DGlcpAb1-4DGlcpNSa1-4LIdopA[2S]a1-4 (GlcNS-GlcA-GlcNS-Idu2S-ROH)

When I try to read it back using leap:

 source leaprc.GLYCAM_06j-1   
 loadamberparams frcmod.glycam06_intraring_doublebond_protonatedacids
 loadamberprep GlcNS_preliminary.prep
 loadamberprep uronic_acids.prep
 loadoff GLYCAM_aminoct_06j_12SB.lib 
 loadamberprep IdoA_ALL.prep
 hepc = loadpdb 1_AMBER_noh.pdb

I get the following error:

Loading PDB file: ./1_AMBER_noh.pdb
ERROR: Comparing atoms
        .R<0YS 5>.A<C2 3>, 
        .R<0YS 5>.A<H1 2>, 
        .R<4ZB 4>.A<O4 19>, and 
        .R<0YS 5>.A<O5 16> 
       to atoms
        .R<0YS 5>.A<C2 3>, 
        .R<SO3 1>.A<S1 1>, 
        .R<0YS 5>.A<H1 2>, and 
        .R<4ZB 4>.A<O4 19> 
       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 !

If I run the prmtop and crd though cpptraj it fixes the sulfate from the Idu at position 6 bringing it back to position 5. But I'm not sure that that's the way to do it.

Thanks for the help and happy Easter!

Best,

Tarsis