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 - 08:30:04 PDT
