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Hi again,

I see you have a co-complex, so building the carbohydrate on glycam.org
won't help you. Nor will building from sequence. You'll need to reformat
the carbohydrate in 1LZJ in GLYCAM nomenclature so that tleap can recognise
it and bond it correctly. Try reorganizing the atoms so the autobonding
works. Send all the output from tleap if not.

Oliver


On Wed, Oct 31, 2018 at 2:52 PM Oliver Grant <[log in to unmask]> wrote:

> Hi Aarya,
>
> Don't use acpype, unless they have explicitly said that they've updated it
> to work with GLYCAM. Some terms won't get converted.
>
> You can build the structure on glycam.org/cb and click "download all
> structures". You'll get the parameter and rst files in the zip file.
>
> The sequence command in leap is for building from prep files. You could do
> it that way if you want. But note it should be: { ROH 2LB 0fA }. 1fA
> doesn't make sense there.  More detailed examples are the amber manual.
>
> If you load try2.pdb into leap, the issue might be that leap will bond the
> last atom in a residue to the first atom in the next residue, so order the
> atoms in the PDB file according to how you want the residues to be
> auto-bonded by leap (i.e. put the O2 as the last entry for residue 2LB), or
> put TER cards and use the "bond" command (useful for branched
> carbohydrates). I'd need to see your leap output to help further.
>
> Best,
>
> Oliver
>
>
> On Wed, Oct 31, 2018 at 2:37 PM Aarya Venkat <[log in to unmask]> wrote:
>
>> Hi everyone!
>>
>> I am attempting to run an MD in GROMACS on a *co-crystallized*
>> Glycosyltransferase containing a carbohydrate ligand bound.
>>
>> The ligand is a-L-Fucp-(1-2)-B-D-Galp.
>>
>> My structure is 1LZJ is from: https://www.rcsb.org/structure/1LZJ
>>
>> To parametrize this ligand, I am using a combination of tleap and either
>> acpype or Glycam2gmx.pl to convert the amber parm/crd outputs into gromacs
>> format, but neither are giving me working input files (fails at generating
>> ions due to topology incompatibility/Glycam2gmx output finds no residues,
>> where acpype does find residues).
>>
>> I have attached my ligand/PDB as well as crd and top files from tleap.
>>
>> I am thinking this may be due to my tleap file. While it outputs the
>> files without error, I am concerned that I am perhaps not including
>> something here.
>>
>> My code is simply:
>>
>> ####
>> *source leaprc.GLYCAM_06j-1*
>>
>> *loadamberprep GLYCAM_06j-1.prep *
>> *mol = loadpdb try2.pdb*
>> *saveamberparm mol nacc.parm7 nacc.rst7*
>>
>> *#### *
>>
>> I have seen others build sequences from their tleap.
>>
>> ie: seq1 = sequence { ROH 2LB 1fA }
>>
>> I wasn't sure if I had to do this given that I loaded the pdb in. Please
>> let me know if you need any other information. I would appreciate any
>> advice you have. Thank you!
>>
>>
>> Kind regards,
>>
>> Aarya Venkat
>>
>