Dan
I added the line parm protein.prmtop, but I did not get
strip.protein.prmtop.
said
On Wed, Jan 7, 2015 at 8:05 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I just noticed that the file name in the last error message you posted
> reads as "protein.prmtop*", which isn't a valid file name (for a
> single file). See what happens if you put the line:
>
> parm protein.prmtop
>
> at the beginning of your input script and execute cpptraj like so:
>
> cpptraj -i input.file
>
> where 'input.file' contains your script.
>
> -Dan
>
> On Wed, Jan 7, 2015 at 10:42 AM, Ibrahim Said <saidibrahim569.gmail.com>
> wrote:
> > 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
> >> > _______________________________________________
> >> > 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
> >>
> > _______________________________________________
> > 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
>
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Received on Wed Jan 07 2015 - 11:30:02 PST
