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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:

> 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
>