Dear all,

I am currently working on the simulation study of a complex whose ligand cannot be automatically parameterized. I have been using AMBER to do the parameterization, and now I have obtained the .lib for the ligand. I want to load the parameter to the complex to prepare the input file for simulation. After changing the residue and chain name of the ligand in the complex PDB, I did:

tleap -f oldff/leaprc.ff99SB

>source leaprc.gaff

>loadamberparams deoxyFeb.frcmod

>loadoff deo.lib

>complex = loadpdb deoxyCom.pdb

and it added missing heavy atoms that are not included in the parameter lib. (the whole message is as tleap.txt)

how should I deal with the problem and prepare the input file for MD?