Hi,
Pay particular attention to error messages. I find it helpful after
running cpptraj to grep for 'Error' and 'Warning' in my output. In
your case the problem is here:
On Thu, Jan 8, 2015 at 5:03 AM, Ibrahim Said <saidibrahim569.gmail.com> wrote:
> Error: unknown symbol ==.== in residue name parsing.
> Mask [:1-185.CA] represents 0 atoms !!!NO ATOMS DETECTED!!!
":1-185.CA" is not a valid atom mask. The '.' symbol denotes atoms, so
the mask should be ":1-185.CA". I highly recommend you read the
section of the manual devoted to atom masks in Amber to become more
familiar with the syntax (section 7.2.2 in the AmberTools 12 manual,
section 28.2.3 in the Amber 14 manual).
-Dan
> ATOMICFLUCT: dumping atomic positional fluctuations by atom to file
> chain1.fluct.dat
> Atom selection [No atoms are selected]
> 2: [rms ref [chain2] :186-366 :1-185]
> Warning: # atoms in active reference frame (2925) < # atoms in current
> topology strip.1blb_dimer.prmtop (5783). Distance-based mask
> parsing will not work.
> 2858 atoms selected.
> 3: [atomicfluct out chain2.fluct.dat :186-366.CA byatom]
> Warning: # atoms in active reference frame (2925) < # atoms in current
> topology strip.1blb_dimer.prmtop (5783). Distance-based mask
> parsing will not work.
> Error: unknown symbol ==.== in residue name parsing.
> Mask [:186-366.CA] represents 0 atoms !!!NO ATOMS DETECTED!!!
> ATOMICFLUCT: dumping atomic positional fluctuations by atom to file
> chain2.fluct.dat
> Atom selection [No atoms are selected]
> ----- [strip.md.nc] (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 1000 frames and processed 1000 frames.
>
> ACTION OUTPUT:
> PTRAJ ATOMICFLUCT: Dumping atomic positional fluctuations
> Segmentation fault (core dumped)
>
> Please, can you help me.
>
> said
>
>
>
> On Wed, Jan 7, 2015 at 11:53 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> First, I didn't mention this before but you had mentioned you're using
>> Amber 12. I highly recommend you use cpptraj from AmberTools 14 for
>> analysis (http://ambermd.org/AmberTools14-get.html).
>>
>> Second, it's not clear what input you are using when you do not get
>> your stripped topology. In general when you have an issue with cpptraj
>> it's best to post *exactly* what you ran: command and all lines of
>> input. Otherwise we have to guess at what's going wrong which is
>> usually not productive.
>>
>> Based on the input you provided before and the recommendations I made,
>> you should be running something like this:
>>
>> parm 1blb_dimer.prmtop
>> trajin 1blb_dimer-prod-1.mdcrd 1 50 1
>> strip :WAT,Na+ outprefix strip
>> trajout strip.md.nc netcdf
>>
>> This should produce 'strip.1blb_dimer.prmtop' which is your stripped
>> topology file and 'strip.md.nc' which is your stripped trajectory
>> file. Were either of these files not generated? Or did you perhaps use
>> different input?
>>
>> -Dan
>>
>> On Wed, Jan 7, 2015 at 1:33 PM, Ibrahim Said <saidibrahim569.gmail.com>
>> wrote:
>> > Dear Dan
>> > This is the first error I have faced. cpptraj can not write this
>> > strip.1blb_dimer.prmtop.
>> >
>> > said
>> >
>> > On Wed, Jan 7, 2015 at 10:26 PM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>> >
>> >> Sorry, you need to use the stripped topology of course:
>> >>
>> >> > parm 1blb_dimer.prmtop
>> >>
>> >> should instead be
>> >>
>> >> parm strip.1blb_dimer.prmtop
>> >>
>> >> which should have been generated in the previous step.
>> >>
>> >> -Dan
>> >>
>> >> > trajin strip.md.nc
>> >> > rms :1-185 first
>> >> > average chain1.pdb :1-185 pdb
>> >> > rms :186-366 first
>> >> > average chain2.pdb :186-366 pdb
>> >> >
>> >> > -Dan
>> >> >
>> >> > On Wed, Jan 7, 2015 at 12:39 PM, Ibrahim Said <
>> saidibrahim569.gmail.com>
>> >> wrote:
>> >> >> Dear Dan
>> >> >> My full script is
>> >> >> parm 1blb_dimer.prmtop
>> >> >> trajin 1blb_dimer-prod-1.mdcrd 1 50 1
>> >> >> -
>> >> >> -
>> >> >> -
>> >> >> strip :WAT
>> >> >> strip :Na+
>> >> >> average chain1.pdb :1-185 pdb
>> >> >> average chain2.pdb :186-366 pdb
>> >> >> trajout strip.md.nc netcdf
>> >> >> Also I did not see the previous massage.
>> >> >>
>> >> >> said
>> >> >>
>> >> >> On Wed, Jan 7, 2015 at 9:33 PM, David A Case <
>> case.biomaps.rutgers.edu>
>> >> >> wrote:
>> >> >>
>> >> >>> On Wed, Jan 07, 2015, Ibrahim Said wrote:
>> >> >>>
>> >> >>> > I added the line parm protein.prmtop, but I did not get
>> >> >>> > strip.protein.prmtop.
>> >> >>>
>> >> >>> This sounds like progress, assuming that all the other error
>> messages
>> >> >>> (relating to not being able to open the protein.prmtop file) are
>> gone.
>> >> >>>
>> >> >>> > > > trajin 1blb_dimer-prod-1.mdcrd 1 50 1
>> >> >>> > > > -
>> >> >>> > > > -
>> >> >>> > > > -
>> >> >>> > > > trajin 1blb_dimer-prod-12.mdcrd 1 100 1
>> >> >>> > > > trajout strip.md.nc netcdf
>> >> >>>
>> >> >>> The above script doesn't have any "strip" commands in it. Are you
>> >> actually
>> >> >>> expecting to strip atoms?
>> >> >>>
>> >> >>> If you want to get a stripped prmtop file (in addition to a stripped
>> >> >>> trajectory file), you need to have a "strip" line with the
>> "outprefix"
>> >> >>> option.
>> >> >>> (And if you just want to combine several trajectory files into a
>> single
>> >> >>> one,
>> >> >>> without stripping atoms, then there is no need to create a new
>> prmtop
>> >> >>> file.)
>> >> >>>
>> >> >>> ...hope this helps...dac
>> >> >>>
>> >> >>>
>> >> >>> _______________________________________________
>> >> >>> 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)
>> >>
>> >>
>> >>
>> >> --
>> >> -------------------------
>> >> 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
>>
> _______________________________________________
> 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)
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Received on Thu Jan 08 2015 - 08:30:03 PST
