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)
>> >
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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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Received on Fri Jul 29 2016 - 14:00:04 PDT
