I expect 100 frames for each protein : 400 frames (in total)..
But, I get 400 frames for each protein : 1600 ( in total)
Here, I attach the output file
**********************************************
Hirdesh Kumar
PhD (Molecular Parasitology), MS (Pharmacoinformatics), B. Pharm
AG Frischknecht
*Parasitology - Center for Infectious Diseases*
*University of Heidelberg Medical School*
*Im Neuenheimer Feld 324*
*69120 HeidelbergGermany*
Lab number
:
+49 (0)6221 567438
Mobile number: +49(0) 176 83517413
**********************************************
On Fri, Jul 29, 2016 at 11:27 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> According to the output in cpptraj.log (pasted below), you are reading
> 100 frames as requested from 4 trajectories, so the total number of
> frames processed is 400. So I'm not sure what the issue is.
>
> ```
> INPUT TRAJECTORIES:
> 0: 'WT.mdcrd' is an AMBER trajectory, Parm WT.prmtop (Trunc. Oct.
> box) (reading 100 of 50100)
> 1: 'GFP.mdcrd' is an AMBER trajectory, Parm GFP.prmtop (Trunc. Oct.
> box) (reading 100 of 50100)
> 2: 'MIC.mdcrd' is an AMBER trajectory, Parm MIC.prmtop (Trunc. Oct.
> box) (reading 100 of 50008)
> 3: 'mCherry.mdcrd' is an AMBER trajectory, Parm mCherry.prmtop
> (Trunc. Oct. box) (reading 100 of 50100)
> Coordinate processing will occur on 400 frames.
> ```
>
> On Fri, Jul 29, 2016 at 3:25 PM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
> wrote:
> > *Here I attach the input file and log file*
> >
> > On Fri, Jul 29, 2016 at 11:20 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Based on the output you provided from CPPTRAJ previously, it seems
> >> like only 100 frames from each trajectory were being read:
> >>
> >> > 0: 'WT.mdcrd' is an AMBER trajectory, Parm WT.prmtop (Trunc. Oct. box)
> >> (reading 100 of 50100)
> >>
> >> etc.
> >>
> >> -Dan
> >>
> >> On Fri, Jul 29, 2016 at 3:09 PM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
> >> wrote:
> >> > Thanks Daniel..
> >> >
> >> > I
> >> > got
> >> > one more problem:
> >> >
> >> >
> >> > Although I selected just 100 frames of each trajectory. There are 400
> >> > frames for each protein.
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > **
> >> >
> >> > On Fri, Jul 29, 2016 at 10:45 PM, Daniel Roe <daniel.r.roe.gmail.com>
> >> wrote:
> >> >
> >> >> You forgot the 'parm' keywords in your trajin commands (e.g. trajin
> >> >> GFP.mdcrd parm GFP.prmtop etc).
> >> >>
> >> >> -Dan
> >> >>
> >> >> On Fri, Jul 29, 2016 at 1:52 PM, Hirdesh Kumar <
> hirdesh.iitd.gmail.com>
> >> >> wrote:
> >> >> > Thanks Dan and others..
> >> >> >
> >> >> > I tried following script in cpptraj..
> >> >> >
> >> >> > parm WT.prmtop
> >> >> > parm GFP.prmtop
> >> >> > parm MIC.prmtop
> >> >> > parm mCherry.prmtop
> >> >> > trajin WT.mdcrd
> >> >> > trajin GFP.mdcrd
> >> >> > trajin MIC.mdcrd
> >> >> > trajin mCherry.mdcrd
> >> >> > reference WT.mdcrd 1 parm WT.prmtop [wt]
> >> >> > reference GFP.mdcrd 1 parm GFP.prmtop [gfp]
> >> >> > reference MIC.mdcrd 1 parm MIC.prmtop [mic]
> >> >> > reference mCherry.mdcrd 1 parm mCherry.prmtop [mch]
> >> >> > rms WT ref [wt] :1-88.C,CA,N,O out rmsd.dat
> >> >> > rms GFP ref [gfp] :1-88.C,CA,N,O out rmsd.dat
> >> >> > rms MIC ref [mic] :1-88.C,CA,N,O out rmsd.dat
> >> >> > rms mCherry ref [mch] :258-345.C,CA,N,O out rmsd.dat
> >> >> >
> >> >> > But, I am sure something is wrong.. Because at step 1, rmsd value
> is
> >> not
> >> >> > zero for each case:
> >> >> >
> >> >> > #Frame WT GFP MIC
> >> >> > 1 0.0000 0.7683 0.6705
> >> >> >
> >> >> >
> >> >> > In the log file, I found that all trajectories were read using
> single
> >> >> > "WT.prmtop" file:
> >> >> >
> >> >> > INPUT TRAJECTORIES:
> >> >> > 0: 'WT.mdcrd' is an AMBER trajectory, Parm WT.prmtop (Trunc. Oct.
> >> box)
> >> >> > (reading 100 of 50100)
> >> >> > 1: 'GFP.mdcrd' is an AMBER trajectory, Parm WT.prmtop (reading
> 100 of
> >> >> > 179366)
> >> >> > 2: 'MIC.mdcrd' is an AMBER trajectory, Parm WT.prmtop (reading
> 100 of
> >> >> > 71554)
> >> >> > 3: 'mCherry.mdcrd' is an AMBER trajectory, Parm WT.prmtop (reading
> >> 100
> >> >> of
> >> >> > 185989)
> >> >> > Coordinate processing will occur on 400 frames.
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> > On Fri, Jul 29, 2016 at 9:02 PM, Hai Nguyen <nhai.qn.gmail.com>
> >> wrote:
> >> >> >
> >> >> >> . Hirdesh:
> >> >> >>
> >> >> >> adding to Dan's comment about cpptraj's flexibility: use can
> design
> >> >> their
> >> >> >> own protocol with pytraj ( :D )
> >> >> >>
> >> >> >> # Python stuff
> >> >> >> import pytraj as pt
> >> >> >>
> >> >> >> all_rmsd = [ ]
> >> >> >>
> >> >> >> for (fn, parm_name) in [('A.mdcrd', 'A.parm'),
> >> >> >> ('B.mdcrd', 'B.parm'),
> >> >> >> ('C.mdcrd', 'C.parm')]:
> >> >> >>
> >> >> >> traj = pt.iterload(fn, top=parm_name)
> >> >> >> # ref=0: first frame
> >> >> >> # ref=-1: last frame
> >> >> >> # and so on.
> >> >> >> rmsd_data = pt.rmsd(traj, ref=0)
> >> >> >> all_rmsd.append(rmsd_data)
> >> >> >>
> >> >> >> Hai
> >> >> >>
> >> >> >> On Fri, Jul 29, 2016 at 11:36 AM, Daniel Roe <
> daniel.r.roe.gmail.com
> >> >
> >> >> >> wrote:
> >> >> >>
> >> >> >> > On Fri, Jul 29, 2016 at 9:30 AM, Carlos Simmerling
> >> >> >> > <carlos.simmerling.gmail.com> wrote:
> >> >> >> > > my guess is that cpptraj is not set up to load an arbitrary
> >> number
> >> >> of
> >> >> >> > > prmtop files,
> >> >> >> >
> >> >> >> > Cpptraj can load as many topology files as memory will allow.
> >> Loading
> >> >> >> > multiple topology files was actually one of my primary
> motivations
> >> for
> >> >> >> > writing cpptraj in the first place :-)
> >> >> >> >
> >> >> >> > -Dan
> >> >> >> >
> >> >> >> > --
> >> >> >> > -------------------------
> >> >> >> > 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
> >> >> >> >
> >> >> >> _______________________________________________
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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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> >> >>
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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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> > 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)
>
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> AMBER mailing list
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- application/octet-stream attachment: rmsd.dat
Received on Fri Jul 29 2016 - 15:00:02 PDT
