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Hi Oliver,

Thanks a lot, that works.

All the best,

Tarsis

On Sun, Apr 1, 2018 at 3:22 AM, Oliver Grant <[log in to unmask]> wrote:

> 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
>>
>


-- 
Tarsis Gesteira