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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.


Oliver


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

> 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
>