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-1loadamberprep GLYCAM_06j-1.prep
mol = loadpdb try2.pdbsaveamberparm 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