AMBER Archive (2009)

Subject: [AMBER] Load protein complex to Xleap (Combine)

From: Rilei Yu (
Date: Fri Mar 27 2009 - 21:30:04 CDT

Dear anyone who may concern this letter,
I want to perform MD on my protein complex which consits an organic molecue and a receptor. As there is no field paremeters for this organic molecue, I used ANTECHAMBER to obtain the org.prepin and org.frcmod files. Then I obtained the ptomtop and inpcrd successfully, but I still have some problems. After load org and receptor to xleap I find the org (Ligand) was not in the binding cavity. My operation is as follows:
source leaprc.gaff
loadamberprep org.prepin
loadamberparams org.frcmod
#(i found a new unit named M_1 was added to the list)
a = M_1
b = loadpdb receptor.pdb #Only a receptor
c = combine {a,b}
saveamberparm c procomplex.prmtop procomplex.inpcrd
#All went smoothly
edit c
#This time I found the ligand (org) was not in the binding pocket of the receptor.
#Can anyone give some help to solve my problem?
Is there any way that can obtain the accurate procomplex.prmtop and procomplex.inpcrd in which the ligand is accurately positioned by loading the org and receptor respectively?
(I can load the complex accurately by loading  the procomplex directly, but now I want to load the receptor and ligand respectively!)

Rilei Yu

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