I loaded the stripped prmtop file with "file type - AMBER7 Parm" and then
loaded the combined mdcrd file with " file type - Amber coordinates".
Here is the log file when I extract pdb from combined traj.
CPPTRAJ: Trajectory Analysis. V14.25
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
Reading 'strip.Model3_solvated.prmtop' as Amber Topology
INPUT: Reading Input from STDIN
[trajin allProd_dry.mdcrd 3568 3568 1]
Reading 'allProd_dry.mdcrd' as Amber Trajectory
[trajout struct_like_avg.pdb pdb]
Writing 'struct_like_avg.pdb' as PDB
[go ]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES:
0: 'strip.Model3_solvated.prmtop', 2267 atoms, 144 res, box: Orthogonal, 1
mol, 1 frames
INPUT TRAJECTORIES:
0: 'allProd_dry.mdcrd' is an AMBER trajectory, Parm
strip.Model3_solvated.prmtop (Orthogonal box) (reading 1 of 5000)
Coordinate processing will occur on 1 frames.
OUTPUT TRAJECTORIES:
'struct_like_avg.pdb' is a PDB file, Parm strip.Model3_solvated.prmtop:
Writing 1 frames (1-Last, 1)
TIME: Run Initialization took 0.0000 seconds.
BEGIN TRAJECTORY PROCESSING:
----- allProd_dry.mdcrd (3568-3568, 1) -----
100% Complete.
Warning: PDB space group is set to P 1 by default.
Read 1 frames and processed 1 frames.
TIME: Trajectory processing: 0.0137 s
TIME: Avg. throughput= 73.2547 frames / second.
ACTION OUTPUT:
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.0357 seconds.
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
Theory Comput., 2013, 9 (7), pp 3084-3095.
On 12 June 2015 at 11:49, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Are you loading your trajectory into vmd as amber coordinates with periodic
> box? What happens if you load the combined traj back into cpptraj?
>
> On Thursday, June 11, 2015, Soong Jiaxin <jiaxinsoong.gmail.com> wrote:
>
> > Yes, I know it from VMD. I am puzzled too as the cpptraj's output shows
> > 5000 frames.
> >
> > On 12 June 2015 at 11:39, Hai Nguyen <nhai.qn.gmail.com <javascript:;>>
> > wrote:
> >
> > > hi,
> > > how can you tell the combined traj has only 4989 frames (from vmd?) ? I
> > > only see 5000 frames in the cpptraj's output.
> > >
> > > Hai
> > >
> > > On Thu, Jun 11, 2015 at 11:29 PM, Soong Jiaxin <jiaxinsoong.gmail.com
> > <javascript:;>>
> > > wrote:
> > >
> > > > This is the log file for stripping the water and ions. I stripped
> each
> > of
> > > > the mdcrd file one by one.
> > > >
> > > > CPPTRAJ: Trajectory Analysis. V14.25
> > > > ___ ___ ___ ___
> > > > | \/ | \/ | \/ |
> > > > _|_/\_|_/\_|_/\_|_
> > > > Reading '../Model3_solvated.prmtop' as Amber Topology
> > > > INPUT: Reading Input from STDIN
> > > > [trajin ../Prod1.mdcrd]
> > > > Reading '../Prod1.mdcrd' as Amber Trajectory
> > > > [autoimage]
> > > > AUTOIMAGE: To box center based on center of mass, anchor is first
> > > > molecule.
> > > > [strip :WAT]
> > > > STRIP: Stripping atoms in mask [:WAT]
> > > > [strip :Na+ ]
> > > > STRIP: Stripping atoms in mask [:Na+]
> > > > [trajout Prod1_a_dry.mdcrd ]
> > > > Writing 'Prod1_a_dry.mdcrd' as Amber Trajectory
> > > > ---------- RUN BEGIN
> -------------------------------------------------
> > > >
> > > > PARAMETER FILES:
> > > > 0: '../Model3_solvated.prmtop', 34928 atoms, 11035 res, box:
> > Orthogonal,
> > > > 10892 mol, 10885 solvent, 1000 frames
> > > >
> > > > INPUT TRAJECTORIES:
> > > > 0: 'Prod1.mdcrd' is an AMBER trajectory, Parm
> > ../Model3_solvated.prmtop
> > > > (Orthogonal box) (reading 1000 of 1000)
> > > > Coordinate processing will occur on 1000 frames.
> > > >
> > > > OUTPUT TRAJECTORIES:
> > > > 'Prod1_a_dry.mdcrd' is an AMBER trajectory, Parm
> > > > ../Model3_solvated.prmtop: Writing 1000 frames (1-Last, 1)
> > > > TIME: Run Initialization took 0.0000 seconds.
> > > >
> > > > BEGIN TRAJECTORY PROCESSING:
> > > > .....................................................
> > > > ACTION SETUP FOR PARM '../Model3_solvated.prmtop' (3 actions):
> > > > 0: [autoimage]
> > > > Anchor molecule is 1
> > > > 10891 molecules are mobile.
> > > > 1: [strip :WAT]
> > > > Stripping 32655 atoms.
> > > > Stripped parm: '../Model3_solvated.prmtop', 2273 atoms, 150 res,
> > box:
> > > > Orthogonal, 7 mol
> > > > 2: [strip :Na+ ]
> > > > Stripping 6 atoms.
> > > > Stripped parm: '../Model3_solvated.prmtop', 2267 atoms, 144 res,
> > box:
> > > > Orthogonal, 1 mol
> > > > ----- Prod1.mdcrd (1-1000, 1) -----
> > > > 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> > > >
> > > > Read 1000 frames and processed 1000 frames.
> > > > TIME: Trajectory processing: 26.5565 s
> > > > TIME: Avg. throughput= 37.6556 frames / second.
> > > >
> > > > ACTION OUTPUT:
> > > > ---------- RUN END
> ---------------------------------------------------
> > > > TIME: Total execution time: 26.6943 seconds.
> > > >
> > > >
> > >
> >
> --------------------------------------------------------------------------------
> > > > To cite CPPTRAJ use:
> > > > Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ:
> Software
> > > for
> > > > Processing and Analysis of Molecular Dynamics Trajectory Data". J.
> > > Chem.
> > > > Theory Comput., 2013, 9 (7), pp 3084-3095.
> > > >
> > > >
> > > >
> > > > This is the cpptraj log file for combining the mdcrd files:
> > > >
> > > >
> > > > CPPTRAJ: Trajectory Analysis. V14.25
> > > > ___ ___ ___ ___
> > > > | \/ | \/ | \/ |
> > > > _|_/\_|_/\_|_/\_|_
> > > > Reading 'strip.Model3_solvated.prmtop' as Amber Topology
> > > > INPUT: Reading Input from STDIN
> > > > [trajin Prod1_a_dry.mdcrd]
> > > > Reading 'Prod1_a_dry.mdcrd' as Amber Trajectory
> > > > [trajin Prod2_a_dry.mdcrd]
> > > > Reading 'Prod2_a_dry.mdcrd' as Amber Trajectory
> > > > [trajin Prod3_a_dry.mdcrd]
> > > > Reading 'Prod3_a_dry.mdcrd' as Amber Trajectory
> > > > [trajin Prod4_a_dry.mdcrd]
> > > > Reading 'Prod4_a_dry.mdcrd' as Amber Trajectory
> > > > [trajin Prod5_a_dry.mdcrd]
> > > > Reading 'Prod5_a_dry.mdcrd' as Amber Trajectory
> > > > [trajout allProd_dry.mdcrd]
> > > > Writing 'allProd_dry.mdcrd' as Amber Trajectory
> > > > [go]
> > > > ---------- RUN BEGIN
> -------------------------------------------------
> > > >
> > > > PARAMETER FILES:
> > > > 0: 'strip.Model3_solvated.prmtop', 2267 atoms, 144 res, box:
> > > Orthogonal, 1
> > > > mol, 5000 frames
> > > >
> > > > INPUT TRAJECTORIES:
> > > > 0: 'Prod1_a_dry.mdcrd' is an AMBER trajectory, Parm
> > > > strip.Model3_solvated.prmtop (Orthogonal box) (reading 1000 of 1000)
> > > > 1: 'Prod2_a_dry.mdcrd' is an AMBER trajectory, Parm
> > > > strip.Model3_solvated.prmtop (Orthogonal box) (reading 1000 of 1000)
> > > > 2: 'Prod3_a_dry.mdcrd' is an AMBER trajectory, Parm
> > > > strip.Model3_solvated.prmtop (Orthogonal box) (reading 1000 of 1000)
> > > > 3: 'Prod4_a_dry.mdcrd' is an AMBER trajectory, Parm
> > > > strip.Model3_solvated.prmtop (Orthogonal box) (reading 1000 of 1000)
> > > > 4: 'Prod5_a_dry.mdcrd' is an AMBER trajectory, Parm
> > > > strip.Model3_solvated.prmtop (Orthogonal box) (reading 1000 of 1000)
> > > > Coordinate processing will occur on 5000 frames.
> > > >
> > > > OUTPUT TRAJECTORIES:
> > > > 'allProd_dry.mdcrd' is an AMBER trajectory, Parm
> > > > strip.Model3_solvated.prmtop: Writing 5000 frames (1-Last, 1)
> > > > TIME: Run Initialization took 0.0000 seconds.
> > > >
> > > > BEGIN TRAJECTORY PROCESSING:
> > > > ----- Prod1_a_dry.mdcrd (1-1000, 1) -----
> > > > 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> > > >
> > > > ----- Prod2_a_dry.mdcrd (1-1000, 1) -----
> > > > 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> > > >
> > > > ----- Prod3_a_dry.mdcrd (1-1000, 1) -----
> > > > 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> > > >
> > > > ----- Prod4_a_dry.mdcrd (1-1000, 1) -----
> > > > 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> > > >
> > > > ----- Prod5_a_dry.mdcrd (1-1000, 1) -----
> > > > 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> > > >
> > > > Read 5000 frames and processed 5000 frames.
> > > > TIME: Trajectory processing: 32.0629 s
> > > > TIME: Avg. throughput= 155.9433 frames / second.
> > > >
> > > > ACTION OUTPUT:
> > > > ---------- RUN END
> ---------------------------------------------------
> > > > TIME: Total execution time: 32.0862 seconds.
> > > >
> > > >
> > >
> >
> --------------------------------------------------------------------------------
> > > > To cite CPPTRAJ use:
> > > > Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ:
> Software
> > > for
> > > > Processing and Analysis of Molecular Dynamics Trajectory Data". J.
> > > Chem.
> > > > Theory Comput., 2013, 9 (7), pp 3084-3095.
> > > >
> > > > My production is 5ns long. The following is the input file which I
> > > repeated
> > > > the step for 5 times.
> > > >
> > > > Prod Model3
> > > > &cntrl
> > > > imin=0, ntx=5, irest=1,
> > > > nstlim=500000, dt=0.002,
> > > > ntf=2, ntc=2,
> > > > ntpr=100, ntwx=500,
> > > > cut=8.0, ntb=2,
> > > > ntp=1, ntt=1,
> > > > iwrap=1,
> > > > taup=2.0,
> > > > temp0=300.0, tempi=300.0,
> > > > ig=-1,
> > > > /
> > > >
> > > > On 12 June 2015 at 11:14, Hai Nguyen <nhai.qn.gmail.com
> <javascript:;>>
> > wrote:
> > > >
> > > > > hi
> > > > >
> > > > > On Thu, Jun 11, 2015 at 10:48 PM, Soong Jiaxin <
> > jiaxinsoong.gmail.com <javascript:;>>
> > > > > wrote:
> > > > >
> > > > > > Hi all,
> > > > > >
> > > > > > I'm facing problem with my stripped combined mdcrd files. I found
> > out
> > > > > that
> > > > > > the number of frames has been reduced from 5000 frames to 4989
> > frames
> > > > > after
> > > > > > stripping the water molecules and ions.
> > > > >
> > > > >
> > > > > can you post the cpptraj's output + your system info, ...?
> > > > >
> > > > >
> > > > > > Other than that, I also discovered
> > > > > > that the size of combined mdcrd files post stripping is 275.6MB.
> > > > However,
> > > > > > the size of combined mdcrd files before stripping is 4.2GB.
> > > > >
> > > > >
> > > > > yes, the size of water-stripped traj should be much smaller.
> > > > >
> > > > >
> > > > > > My concern is
> > > > > > this normal or is it going to affect my result when I used the
> > > stripped
> > > > > > files to extract the average structure? How do I solve this
> > problem?
> > > > > >
> > > > > > I'd appreciate any help or comment.
> > > > > >
> > > > > > Vanessa.
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org <javascript:;>
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org <javascript:;>
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org <javascript:;>
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org <javascript:;>
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 11 2015 - 21:30:02 PDT
