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