Alright, I've managed to solve the problem. Thank you so much! =)
On 12 June 2015 at 12:17, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Thursday, June 11, 2015, Soong Jiaxin <jiaxinsoong.gmail.com> wrote:
>
> > I loaded the stripped prmtop file with "file type - AMBER7 Parm" and
> then
> > loaded the combined mdcrd file with " file type - Amber coordinates".
>
>
> As you can see from the cpptraj output, your combined trajectroy has box
> info. VMD does not automatically detect this so you must load the
> trajectory as 'Amber coordinates with box info" (or something like that).
> Alternatively, 1) write your combined trajectory without box info by
> specifying 'nobox', or use Netcdf trajectories (personally I would go with
> option 2 as netcdf is superior in practically every way).
>
>
> > 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
> > <javascript:;>> 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
> > <javascript:;>> 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:;>
> > <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:;>
> > > > <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:;>
> > > <javascript:;>>
> > > > wrote:
> > > > > >
> > > > > > > hi
> > > > > > >
> > > > > > > On Thu, Jun 11, 2015 at 10:48 PM, Soong Jiaxin <
> > > > jiaxinsoong.gmail.com <javascript:;> <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
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> > > > > > > >
> > > > > > > _______________________________________________
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> > > > > >
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> > > >
> > >
> > >
> > > --
> > > -------------------------
> > > 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)
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> >
>
>
> --
> -------------------------
> 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
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jun 12 2015 - 00:30:02 PDT
