Hi Tarsis,

tleap was designed for linear sequences of residues like in protein molecules, so it auto-bonds each residue in the sequence it encounters them when reading a PDB file. For branched molecules, you must place a TER card between the residues that should not be bonded to each other (edit the PDB file and literally create a new line with the word "TER", between the residues), and then use the "bond" command in tleap to connect the correct residues to each other. E.g:

mol=loadpdb structure.pdb
bond mol.9.C1 mol.7.O4

That creates a bond between the C1 of residue 9 and the O4 of residue 7. If you've made any mistakes, a good sign is that the charge will not be integral, i.e. it won't be -2.00000 but instead is -1.974. 


On Sat, Dec 15, 2018 at 7:26 AM Tarsis Gesteira <[log in to unmask]> wrote:

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?