Dan,
Thanks for your reply. My version is amber 12.
the script is
trajin 1blb_dimer-prod-1.mdcrd 1 50 1
-
-
-
trajin 1blb_dimer-prod-12.mdcrd 1 100 1
trajout strip.md.nc netcdf
I used cpptraj to calculate Radgyr and RMSD
thank you,
said
On Wed, Jan 7, 2015 at 7:26 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi.
>
> What was your exact input to cpptraj, what version of cpptraj are you
> using (output of cpptraj --version), and are you able to open the file
> 'protein.prmtop' in other programs as well?
>
> -Dan
>
> On Wed, Jan 7, 2015 at 10:04 AM, Ibrahim Said <saidibrahim569.gmail.com>
> wrote:
> > Dear Amber users
> > I am running cpptraj to calculate the RMSF in two steps: the first step
> is
> > ok except I can not get [parm protein.prmtop]. I got the following masage
> >
> >
> > *Error: CpptrajFile::SetupFile: NULL filename specified on READ or
> > APPENDError setting up parm file protein.prmtop for read.Error: Could not
> > open parm protein.prmtop*
> > please, how can I overcome this problem
> >
> > said
> > _______________________________________________
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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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>
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Received on Wed Jan 07 2015 - 10:00:03 PST
