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
>> >> >
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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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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Received on Fri Jul 29 2016 - 14:30:03 PDT
