Hello all
I am attempting to run MMPBSA by triple trajectory approach.
I have three seperate trajectory for complex, receptor and ligand.
When I am using these trajectory to run MMPBSA.py, ptraj is not able to
read frame in receprtor and ligand, reading only complex trajectory frame.
I am not getting where is the fualt?
Here is my script:
input file for running GB
&general
startframe=1, endframe=400, verbose=1, strip_mdcrd=0,
/
&gb
igb=2, saltcon=0.100
/
Here is the ptraj.out file
PTRAJ: Processing input from file _MMPBSA_cenptraj.in
PTRAJ: trajin Q50-NPT_strip.mdcrd 1 400 1
Checking coordinates: Q50-NPT_strip.mdcrd
checkCoordinates(): Could not predict number of frames for AMBER trajectory
file: Q50-NPT_strip.mdcrd
If this is not a compressed file then there is a problem
Rank: 0 Atoms: 1836 FrameSize: 44615 TitleSize: 30 NumBox: 0 Seekable 0
PTRAJ: trajin Q50-TG_NPT-strip-400ps.mdcrd 1 400 1
Checking coordinates: Q50-TG_NPT-strip-400ps.mdcrd
Rank: 0 Atoms: 1836 FrameSize: 44640 TitleSize: 30 NumBox: 3 Seekable 1
PTRAJ: trajin TG-NPT_strip.mdcrd 1 400 1
Checking coordinates: TG-NPT_strip.mdcrd
checkCoordinates(): Could not predict number of frames for AMBER trajectory
file: TG-NPT_strip.mdcrd
If this is not a compressed file then there is a problem
Rank: 0 Atoms: 1836 FrameSize: 44615 TitleSize: 30 NumBox: 0 Seekable 0
Can anyone please suggest me where I am doing wrong?
With regards
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Sat Sep 03 2011 - 05:30:03 PDT
