In God we trust
Hello Dear Amber users:
I have done simulation a protein system containing a Ca and Zn atoms and a
docked ligand. I am trying to do an MMPBSA calculation on my protein
complex. I make topologies of complex and ligand and receptor with these
commands in tleap:
tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
addAtomTypes {
{ "C0" "Ca" "sp3" }
}
loadamberparams cal.frcmod
loadoff Ca2.lib
addAtomTypes {
{ "Zn" "Zn" "sp3" }
}
loadamberparams zinc.frcmod
loadoff zn2.lib
REC = loadpdb a2.pdb
bond REC.170.Zn REC.83.NE2
bond REC.170.Zn REC.68.NE2
bond REC.170.Zn REC.96.ND1
bond REC.169.Zn REC.122.NE2
bond REC.169.Zn REC.118.NE2
bond REC.169.Zn REC.128.NE2
bond REC.171.Ca REC.75.OD1
bond REC.171.Ca REC.80.O
bond REC.171.Ca REC.101.OE2
bond REC.171.Ca REC.98.OD2
charge REC
addions2 REC Na+ 0
saveamberparm REC rec.prmtop rec.crd
loadamberprep lig.prepin
saveoff DRG lig.lib
loadamberparams lig.frcmod
loadoff lig.lib
LIG = loadpdb best2f.pdb
saveamberparm LIG lig.prmtop lig.crd
charge COM
COM = combine {REC LIG}
addions2 COM Na+ 0
saveamberparm COM com.prmtop com.crd
###################################################################################
tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
addAtomTypes {
{ "C0" "Ca" "sp3" }
}
loadamberparams cal.frcmod
loadoff Ca2.lib
addAtomTypes {
{ "Zn" "Zn" "sp3" }
}
loadamberparams zinc.frcmod
loadoff zn2.lib
REC = loadpdb a2.pdb
bond REC.170.Zn REC.83.NE2
bond REC.170.Zn REC.68.NE2
bond REC.170.Zn REC.96.ND1
bond REC.169.Zn REC.122.NE2
bond REC.169.Zn REC.118.NE2
bond REC.169.Zn REC.128.NE2
bond REC.171.Ca REC.75.OD1
bond REC.171.Ca REC.80.O
bond REC.171.Ca REC.101.OE2
bond REC.171.Ca REC.98.OD2
loadamberprep lig.prepin
saveoff DRG lig.lib
loadamberparams lig.frcmod
loadoff lig.lib
LIG = loadpdb best2f.pdb
COM = combine {REC LIG}
solvateoct COM TIP3PBOX 12
charge COM
addions2 COM Na+ 0
saveamberparm COM solvated-com.prmtop solvated-comp.crd
I can do MD simulation without error with solvated-com.prmtop , but when I
do MMPBSA caIculations of PB/GB with this command:
MMPBSA.py.MPI -O -i mmpbsa.in -o FINALRESULTS.dat -sp solvated-com.prmtop
-cp com.prmtop -rp rec.prmtop -lp lig.prmtop -y md.inpcrd
I get this error:
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
sander found! Using /usr/local/amber12/bin/sander
mmpbsa_py_energy found! Using /usr/local/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /usr/local/amber12/bin/cpptraj
ptraj found! Using /usr/local/amber12/bin/ptraj
mmpbsa_py_nabnmode found! Using /usr/local/amber12/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...
Error in box coord line of trajectory _MMPBSA_complex.mdcrd.0.
Expect only 3 or 6 box coords.
Problem line: 8.217 8.073 15.249 8.729 7.131 15.447 8.690
8.910
Error: Could not set up _MMPBSA_complex.mdcrd.0 for reading.
Error: trajin: Could not set up trajectory.
TrajError: Trajectory _MMPBSA_complex.mdcrd.0 has 0 frames!
Exiting. All files have been retained.
I work with AmberTools12 and (optionally) Amber12 and here is my mmpbsa.in :
Input file for running PB and GB
&general
receptor_mask=:1-171,
ligand_mask=:172,
strip_mask=":WAT:Na+",
entropy=1,
endframe=25000,
interval=500,
verbose=1,
use_sander=1,
/
&gb
igb=8, saltcon=0.100,
/
&pb
cavity_offset = -0.5692
cavity_surften = 0.0378
exdi = 80.0
fillratio = 4.0
indi = 1.0
inp = 1
istrng = 0.1
linit = 1000
prbrad = 1.4
radiopt = 0
sander_apbs = 0
scale = 2.0
/
&nmode
nmode_igb=1, nmode_istrng=0.10,
/
I Can load the complex topology and trajectory in VMD?
Would you please guide me. What is my error?
Thank you very much for your help.
Karim Mahnam(PhD, Assistant Professor)
Molecular Biophyicis. Biology Dept., Faculty of Sciences, Shahrekod
University, IRAN.
Tel. 098-0381-4424401-5 Fax. 098-0381-4424419
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Received on Thu May 29 2014 - 06:30:02 PDT
