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
>>
> _______________________________________________
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> 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)
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Received on Wed Jan 07 2015 - 10:30:03 PST
