Dear Dan
It is working, Thank you.
I am sorry for confusion. As I told you I am using Amber 12. And for some
technical reasons, I can not upgrade to Ambertools14. Please, I still have
the following problem, the rms should fit to average structure, I get the
following error massage
INPUT: Reading Input from file RMSF_1blb_dimer-phase-B.in
[parm strip.1blb_dimer.prmtop]
Warning: Parm strip.1blb_dimer.prmtop already loaded, skipping.
[trajin strip.md.nc]
[strip.md.nc] contains 1000 frames.
[parm chain1.pdb]
Reading PDB file chain1.pdb as topology file.
[reference chain1.pdb parm chain1.pdb [chain1]]
[chain1.pdb] contains 1 frames.
[parm chain2.pdb]
Reading PDB file chain2.pdb as topology file.
[reference chain2.pdb parm chain2.pdb [chain2]]
[chain2.pdb] contains 1 frames.
[rms ref [chain1] :1-185 :1-185]
[atomicfluct out chain1.fluct.dat :1-185.CA byatom]
[rms ref [chain2] :186-366 :1-185]
[atomicfluct out chain2.fluct.dat :186-366.CA byatom]
INPUT TRAJECTORIES:
[strip.md.nc] is a NetCDF AMBER trajectory, Parm 0 (with box info)
(reading 1000 of 1000)
Coordinate processing will occur on 1000 frames.
PARAMETER FILES:
0: strip.1blb_dimer.prmtop, 5783 atoms, 366 res, ortho. box, 2 mol, 1000
frames
1: chain1.pdb, 2925 atoms, 185 res, no box
2: chain2.pdb, 2858 atoms, 181 res, no box
REFERENCE COORDS:
[chain1.pdb] is a PDB file, Parm 1 (reading 1 of 1)
[chain2.pdb] is a PDB file, Parm 2 (reading 1 of 1)
The following 2 frames have been defined:
0: [chain1] frame 1
1: [chain2] frame 1
Active reference frame for masks is 0
OUTPUT TRAJECTORIES:
No files.
ACTIONS: Initializing 4 actions:
0: [rms ref [chain1] :1-185 :1-185]
RMSD: (:1-185), reference is [chain1] (:1-185), with fitting.
1: [atomicfluct out chain1.fluct.dat :1-185.CA byatom]
PTRAJ ACTION: [atomicfluct]
2: [rms ref [chain2] :186-366 :1-185]
RMSD: (:186-366), reference is [chain2] (:1-185), with fitting.
3: [atomicfluct out chain2.fluct.dat :186-366.CA byatom]
PTRAJ ACTION: [atomicfluct]
BEGIN TRAJECTORY PROCESSING:
.....................................................
PARM [strip.1blb_dimer.prmtop]: Setting up 4 actions.
0: [rms ref [chain1] :1-185 :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.
2925 atoms selected.
1: [atomicfluct out chain1.fluct.dat :1-185.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 [:1-185.CA] represents 0 atoms !!!NO ATOMS DETECTED!!!
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
>
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Received on Thu Jan 08 2015 - 04:30:02 PST
