Dear Amber Users,
I am trying to do MMPBSA calculations with a single trajectory and gives the following error:
----------------------------------------------
Preparing trajectories for simulation...
Error in box coord line of trajectory h3_820_complex_prod2.mdcrd.
Expect only 3 or 6 box coords.
Problem line: 4.509 71.808 82.630 27.602 29.349 36.456 58.340 102.059 -20.666
Error: Could not set up h3_820_complex_prod2.mdcrd for reading.
Error: trajin: Could not set up trajectory.
TrajError: Trajectory h3_820_complex_prod2.mdcrd has 0 frames!
Exiting. All files have been retained.
--------------------------------------------------
I went through the previous user lists messages, but there is no clear answers that I could find.
my input file looks like this:
----------------------------------------
&general
startframe=1, endframe=2500, interval=50,
verbose=2,
/
&gb
igb=5, saltcon=0.150,
Earlier I prepared the input files using the following script
---------------------------------------------------------
source leaprc.ff99SB
loadoff aly.lib
loadamberparams aly.frcmod
lig = loadpdb H3_820_unmodified_ligand.pdb
prot = loadpdb H3_820_unmodified_protein.pdb
complex = combine{prot lig}
set default PBRadii mbondi2
saveamberparm lig h3_820_lig.prmtop h3_820_lig.inpcrd
saveamberparm prot h3_820_protein.prmtop h3_820_protein.inpcrd
saveamberparm complex h3_820_complex.prmtop h3_820_complex.inpcrd
charge complex
addions complex Cl- 0
solvateOct complex TIP3PBOX 16.0
saveamberparm complex h3_820_complex_solvated.prmtop h3_820_complex_solvated.inpcrd
quit
-----------------------------------
I am running MMPBSA.py as follows
MMPBSA.py -O -i h3820_mmpbsa.in -cp h3_820_complex.prmtop -rp h3_820_protein.prmtop -lp h3_820_lig.prmtop -y h3_820_complex_prod2.mdcrd
Any suggestions would be appreciated?
Thanks,
Senthil Natesan
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Received on Thu Jun 06 2013 - 09:00:03 PDT
