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 - 08:30:02 PDT
