Re: [AMBER] MMPBSA_complex.mdcrd.0 error

From: Ray Luo, Ph.D. <ray.luo.uci.edu> Date: Thu, 29 May 2014 10:01:30 -0700

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Thu, May 29, 2014 at 7:03 AM, mahnam karim
<mahnam.karim.sci.sku.ac.ir> wrote:
>
>
>
> 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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