You should just be able to run
cpptraj -i <input file>
since the 'parm' commands in your input file will load the topologies.
If you really wanted to load them from the command line you would use
a '-p' flag for each topology, e.g.
cpptraj -p A.prmtop -p B.prmtop -p C.prmtop -i input
-Dan
On Fri, Jul 29, 2016 at 9:00 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)
>>
>> _______________________________________________
>> 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
Received on Fri Jul 29 2016 - 09:00:03 PDT
