Dear Sir/Madam,
I have to calculate the MM/GBSA binding energy for a protein1-protein2-protein3 complex. My prmtop files are listed in the order of protein1, protein2 and then protein3.
I want to calculate the binding energy of protein2 to the binary complex of protein 1 and protein3. Since protein 1 and protein3 are separated, I cannot define them as one. I have used the following input file for snapshot.in, but how can I define if the receptor is separated into two groups? What's wrong with my input file? Pls kindly instruct. Thank you.
.GENERAL
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./protein1protein2protein3.prmtop
RECPT ./protein1protein3.prmtop
LIGPT ./protein2.prmtop
GC 1
AS 0
DC 0
MM 0
GB 0
PB 0
MS 0
NM 0
.MAKECRD
BOX YES
NTOTAL 108188
NSTART 1
NSTOP 50000
NFREQ 50
NUMBER_LIG_GROUPS 2
LSTART 1
LSTOP 7864
LSTART 11204
LSTOP 12146
NUMBER_REC_GROUPS 1
RSTART 7865
RSTOP 11203
.TRAJECTORY
xxxx.mdcrd.gz
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Received on Wed Dec 08 2010 - 09:00:04 PST
