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
>> >> >> >
>> >> >> _______________________________________________
>> >> >> 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
>> >>
>> >>
>> >>
>> >> --
>> >> -------------------------
>> >> 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
>>
>>
>>
>> --
>> -------------------------
>> 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
>
--
-------------------------
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 - 14:30:04 PDT
