Hi Tarsis,

tleap doesn't automatically handle branching, and will bond each residue to each following residue as it reads it from the pdb file. So you can put a line that says TER in the pdb file in between the parts of your structure that is branched and then use tleap bond commands to bond the parts you want bonded. 

The way I do it is to put TER cards between every residue in the glycan and convert the LINK cards, which glycam generates and puts at the top of the pdb file, into tleap bond commands. It's easier to automate like that, rather than figuring out where the branch points are for each glycan you want to run through tleap.

On Sat, 31 Mar 2018, 23:44 Tarsis Gesteira, <[log in to unmask]> wrote:

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!