my guess is that cpptraj is not set up to load an arbitrary number of
prmtop files, and you may find it easier to write a script that calls
cpptraj for each of your systems, perhaps using some variables for the file
names so the actual cpptraj script can be reused.
On Fri, Jul 29, 2016 at 11:08 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
wrote:
> I have many mutations of the same protein.. and I am looking for a single
> script to do an analysis (say rmsd) for all different systems.
>
> **
>
> On Fri, Jul 29, 2016 at 5:04 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > Can you clarify why you want 1 script to do 3 different rmsd calculations
> > for 3 prmtops and 3 trajectories? Why not run 3 separate scripts? That
> > would seem much easier to me. Am I missing something?
> >
> > On Jul 29, 2016 11:00 AM, "Hirdesh Kumar" <hirdesh.iitd.gmail.com>
> wrote:
> >
> > thanks Danial,
> >
> > Silly question, how should I run the script now:
> > usual format is:
> >
> >
> > *cpptraj -p <top fil> -i <input file>*
> > however, in current case, there are four topology files
> >
> >
> > *I tried:*
> >
> >
> >
> > *cpptraj -p A.prmtop B.prmtop C.prmtop -i rmsd.in <http://rmsd.in>*
> >
> >
> > *Hirdesh*
> >
> > **********************************************
> > 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 4:31 PM, Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > On Fri, Jul 29, 2016 at 6:26 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com
> >
> > > wrote:
> > > >
> > > > rms A first :1-88.C,CA,N rmsd.dat
> > > > rms B first :288-328.C,CA,N rmsd.dat
> > > > rms C first :1-88.C,CA,N rmsd.dat
> > >
> > > You actually need to use the 'out' keyword before your output file
> > > names (i.e. "out rmsd.dat").
> > >
> > > >
> > > > how should I define *first* for each and every trajectory?
> > >
> > > You can use a 'reference' command to explicitly define the first frame
> > > of each trajectory as a reference structure, e.g.:
> > >
> > > parm A.prmtop
> > > trajin A.mdcrd parm A.prmtop
> > > reference A.mdcrd 1 parm A.prmtop [A_first]
> > > ...
> > > rms A ref [A_first] :1-88.C,CA,B out rmsd.dat
> > > ...
> > >
> > > Hope this helps,
> > >
> > > -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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Received on Fri Jul 29 2016 - 09:00:02 PDT
