Hi Mahrukh,
If it's just a few bonds it's quickest to do this manually in tleap. I always use tleap (tleap -f
leap_inputs.in) so I don't know why you're getting missing parameters in xleap.
Both xleap and tleap were designed to handle proteins, which are always linear, and thus the program does not handle branching molecules automatically. To get around this you insert a TER card in the PDB where the non-continuous branches start e.g.:
ATOM 5242 O GLY 507 -12.269 -30.012 -67.337 1.00 0.00
TER
ATOM 2 C1 4YB 508 13.117 -16.557 -28.890 1.00 0.00
the TER is placed there as the 4YB should be connected to an NLN, another e.g.:
ATOM 73 O6 0MA 513 10.408 -11.034 -18.659 1.00 0.00
TER
ATOM 74 C1 2MA 514 17.112 -11.543 -15.725 1.00 0.00
This is where one branch of an N-linked glycan has ended and the next residue is connected to a residue that is listed earlier in the glycan.
With the TER cards tleap will not automatically try to bond the GLY to the 4YB. Instead you can include bond commands in your tleap input file e.g.:
########### Set Defaults ############################## #####################
set default PBRadii mbondi2
############################## ############################## ################
########### Force Field Inputs ############################## ###############
source /cm/shared/apps/amber14/dat/ leap/cmd/leaprc.GLYCAM_06j-1
source /cm/shared/apps/amber14/dat/ leap/cmd/leaprc.ff14SB
loadAmberParams frcmod.tip5p
############################## ############################## ################
########load Carb################
mol=loadpdb structure.pdb
#BONDING
bond mol.101.ND2 mol.508.C1
bond mol.510.O6 mol.514.C1
etc ...
saveamberparm mol CPLX.prmtop CPLX.rst7
savepdb mol CPLX.pdb
#############Addions########## ####
addIons mol Na+ 0
addIons mol Cl- 0
saveamberparm mol CPLX_Neut.prmtop CPLX_Neut.rst7
savepdb mol CPLX_Neut.pdb
#############Solvate########## ####
solvatebox mol TIP5PBOX 10.0
saveamberparm mol CPLX_Neut_Sol.prmtop CPLX_Neut_Sol.rst7
savepdb mol CPLX_Neut_Sol.pdb
quit
I've included my entire tleap file for completeness.
If you have a lot of systems or a lot of N-linked glycans, this is a pain to do. I've semi-automated the process, but it requires you to use some scripts.
Here is a full link to a how-to:
If you try those scripts and they don't work for you, please let me know.