What version of cpptraj are you using? Make sure you are using the most
up-to-date one (from AmberTools 15).
-Dan
On Wed, Jun 24, 2015 at 2:35 PM, bharat lakhani <lakhbharat.gmail.com>
wrote:
> Thanks Dan, But Now that I have fixed it there is segmentation fault. I do
> not know whats went wrong?? Please Advice
>
> 1: [rms reference :1-99.N,CA,C,O :1-99.N,CA,C,O perres perresavg
> perresavg.dat]
> Mask [:1-99.N,CA,C,O] corresponds to 396 atoms.
> perres: Res 1: # atoms in Tgt [4] != # atoms in Ref [16]
> perres: Res 2: # atoms in Tgt [4] != # atoms in Ref [17]
> perres: Res 3: # atoms in Tgt [4] != # atoms in Ref [24]
> perres: Res 4: # atoms in Tgt [4] != # atoms in Ref [24]
> perres: Res 5: # atoms in Tgt [4] != # atoms in Ref [16]
> perres: Res 6: # atoms in Tgt [4] != # atoms in Ref [24]
> perres: Res 7: # atoms in Tgt [4] != # atoms in Ref [19]
> perres: Res 8: # atoms in Tgt [4] != # atoms in Ref [11]
> perres: Res 9: # atoms in Tgt [4] != # atoms in Ref [22]
> perres: Res 10: # atoms in Tgt [4] != # atoms in Ref [21]
> perres: Res 11: # atoms in Tgt [4] != # atoms in Ref [7]
> perres: Res 12: # atoms in Tgt [4] != # atoms in Ref [14]
> perres: Res 13: # atoms in Tgt [4] != # atoms in Ref [15]
> perres: Res 14: # atoms in Tgt [4] != # atoms in Ref [22]
> perres: Res 15: # atoms in Tgt [4] != # atoms in Ref [14]
> perres: Res 16: # atoms in Tgt [4] != # atoms in Ref [19]
> perres: Res 17: # atoms in Tgt [4] != # atoms in Ref [7]
> perres: Res 18: # atoms in Tgt [4] != # atoms in Ref [20]
> perres: Res 19: # atoms in Tgt [4] != # atoms in Ref [21]
> perres: Res 20: # atoms in Tgt [4] != # atoms in Ref [19]
> perres: Res 21: # atoms in Tgt [4] != # atoms in Ref [24]
> perres: Res 22: # atoms in Tgt [4] != # atoms in Ref [12]
> perres: Res 23: # atoms in Tgt [4] != # atoms in Ref [7]
> perres: Res 24: # atoms in Tgt [4] != # atoms in Ref [11]
> perres: Res 25: # atoms in Tgt [4] != # atoms in Ref [11]
> perres: Res 26: # atoms in Tgt [4] != # atoms in Ref [16]
> perres: Res 27: # atoms in Tgt [4] != # atoms in Ref [24]
> perres: Res 28: # atoms in Tgt [4] != # atoms in Ref [16]
> perres: Res 29: # atoms in Tgt [4] != # atoms in Ref [14]
> perres: Res 30: # atoms in Tgt [4] != # atoms in Ref [14]
> perres: Res 31: # atoms in Tgt [4] != # atoms in Ref [17]
> perres: Res 32: # atoms in Tgt [4] != # atoms in Ref [7]
> perres: Res 33: # atoms in Tgt [4] != # atoms in Ref [19]
> perres: Res 34: # atoms in Tgt [4] != # atoms in Ref [15]
> perres: Res 35: # atoms in Tgt [4] != # atoms in Ref [22]
> perres: Res 36: # atoms in Tgt [4] != # atoms in Ref [16]
> perres: Res 37: # atoms in Tgt [4] != # atoms in Ref [14]
> perres: Res 38: # atoms in Tgt [4] != # atoms in Ref [7]
> perres: Res 39: # atoms in Tgt [4] != # atoms in Ref [19]
> perres: Res 40: # atoms in Tgt [4] != # atoms in Ref [20]
> perres: Res 41: # atoms in Tgt [4] != # atoms in Ref [19]
> perres: Res 42: # atoms in Tgt [4] != # atoms in Ref [11]
> perres: Res 43: # atoms in Tgt [4] != # atoms in Ref [24]
> perres: Res 44: # atoms in Tgt [4] != # atoms in Ref [19]
> perres: Res 45: # atoms in Tgt [4] != # atoms in Ref [16]
> perres: Res 46: # atoms in Tgt [4] != # atoms in Ref [14]
> perres: Res 47: # atoms in Tgt [4] != # atoms in Ref [7]
> perres: Res 48: # atoms in Tgt [4] != # atoms in Ref [7]
> perres: Res 49: # atoms in Tgt [4] != # atoms in Ref [19]
> perres: Res 50: # atoms in Tgt [4] != # atoms in Ref [10]
> perres: Res 51: # atoms in Tgt [4] != # atoms in Ref [17]
> perres: Res 52: # atoms in Tgt [4] != # atoms in Ref [11]
> perres: Res 53: # atoms in Tgt [4] != # atoms in Ref [14]
> perres: Res 54: # atoms in Tgt [4] != # atoms in Ref [7]
> perres: Res 55: # atoms in Tgt [4] != # atoms in Ref [19]
> perres: Res 56: # atoms in Tgt [4] != # atoms in Ref [19]
> perres: Res 57: # atoms in Tgt [4] != # atoms in Ref [10]
> perres: Res 58: # atoms in Tgt [4] != # atoms in Ref [16]
> perres: Res 59: # atoms in Tgt [4] != # atoms in Ref [14]
> perres: Res 60: # atoms in Tgt [4] != # atoms in Ref [12]
> perres: Res 61: # atoms in Tgt [4] != # atoms in Ref [15]
> perres: Res 62: # atoms in Tgt [4] != # atoms in Ref [16]
> perres: Res 63: # atoms in Tgt [4] != # atoms in Ref [19]
> perres: Res 64: # atoms in Tgt [4] != # atoms in Ref [15]
> perres: Res 65: # atoms in Tgt [4] != # atoms in Ref [16]
> perres: Res 66: # atoms in Tgt [4] != # atoms in Ref [14]
> perres: Res 67: # atoms in Tgt [4] != # atoms in Ref [7]
> perres: Res 68: # atoms in Tgt [4] != # atoms in Ref [19]
> perres: Res 69: # atoms in Tgt [4] != # atoms in Ref [15]
> perres: Res 70: # atoms in Tgt [4] != # atoms in Ref [16]
> perres: Res 71: # atoms in Tgt [4] != # atoms in Ref [11]
> perres: Res 72: # atoms in Tgt [4] != # atoms in Ref [7]
> perres: Res 73: # atoms in Tgt [4] != # atoms in Ref [22]
> perres: Res 74: # atoms in Tgt [4] != # atoms in Ref [11]
> perres: Res 75: # atoms in Tgt [4] != # atoms in Ref [19]
> perres: Res 76: # atoms in Tgt [4] != # atoms in Ref [12]
> perres: Res 77: # atoms in Tgt [4] != # atoms in Ref [17]
> perres: Res 78: # atoms in Tgt [4] != # atoms in Ref [16]
> perres: Res 79: # atoms in Tgt [4] != # atoms in Ref [14]
> perres: Res 80: # atoms in Tgt [4] != # atoms in Ref [12]
> perres: Res 81: # atoms in Tgt [4] != # atoms in Ref [17]
> perres: Res 82: # atoms in Tgt [4] != # atoms in Ref [17]
> perres: Res 83: # atoms in Tgt [4] != # atoms in Ref [19]
> perres: Res 84: # atoms in Tgt [4] != # atoms in Ref [10]
> perres: Res 85: # atoms in Tgt [4] != # atoms in Ref [14]
> perres: Res 86: # atoms in Tgt [4] != # atoms in Ref [11]
> perres: Res 87: # atoms in Tgt [4] != # atoms in Ref [24]
> perres: Res 88: # atoms in Tgt [4] != # atoms in Ref [14]
> perres: Res 89: # atoms in Tgt [4] != # atoms in Ref [19]
> perres: Res 90: # atoms in Tgt [4] != # atoms in Ref [19]
> perres: Res 91: # atoms in Tgt [4] != # atoms in Ref [19]
> perres: Res 92: # atoms in Tgt [4] != # atoms in Ref [14]
> perres: Res 93: # atoms in Tgt [4] != # atoms in Ref [16]
> perres: Res 94: # atoms in Tgt [4] != # atoms in Ref [24]
> perres: Res 95: # atoms in Tgt [4] != # atoms in Ref [14]
> perres: Res 96: # atoms in Tgt [4] != # atoms in Ref [10]
> perres: Res 97: # atoms in Tgt [4] != # atoms in Ref [14]
> perres: Res 98: # atoms in Tgt [4] != # atoms in Ref [17]
> perres: Res 99: # atoms in Tgt [4] != # atoms in Ref [25]
> 2: [average StructureA_postleap_combi_5-105ns_00001-05050-1-avg1st.pdb
> pdb]
> AVERAGE: Averaging over 396 atoms.
> ----- [1NF3_Par6_pretleap.pdb] (1-1, 1) -----
> 100% Complete.
>
> .....................................................
> ACTION SETUP FOR PARM [1RY4_pretleap_dummy.prmtop] (3 actions):
> 0: [strip !.CA,C,O,N]
> Stripping 1132 atoms.
> Topology StructureB_pretleap_dummy.prmtop contains 396
> atoms.
> 99 residues.
> 395 bonds.
> 1 molecules.
> Box: None
> 1: [rms reference :1-99.N,CA,C,O :1-99.N,CA,C,O perres perresavg
> perresavg.dat]
> Mask [:1-99.N,CA,C,O] corresponds to 396 atoms.
> Warning: DataSet 'RMSD_00000[res]:1' already present.
> Segmentation fault
>
>
> On Wed, Jun 24, 2015 at 3:56 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Hi,
> >
> > On Wed, Jun 24, 2015 at 11:56 AM, bharat lakhani <lakhbharat.gmail.com>
> > wrote:
> >
> > >
> > > rms reference :1-99.N,CA,C,O :1-99.N,CA,O perresavg perresavg.dat
> > >
> >
> > You're missing the 'perres' keyword.
> >
> >
> > >
> > > Also when i use this following line
> > >
> > > rms reference :1-99.N,CA,C,O :1-99.N,CA,O out perresavg.dat
> > >
> >
> > In the first mask you have 'C' atoms, and in the second you don't. That
> > seems to account for the difference between the # of atoms selected
> between
> > the two masks. Either add 'C' to the second mask or remove it from the
> > first.
> >
> > -Dan
> >
> >
> > >
> > > I get this error which does not make sense to me since both proteins
> > > contains same number of residues but different residues since they are
> > > homologous (80% sequence similarity 3A overall rmsd)
> > >
> > >
> > > Mask [:1-99.N,CA,C,O] corresponds to 396 atoms.
> > > Warning: Number of atoms in target mask (396) does not
> > > equal number of atoms in Ref mask (297).
> > > Warning: Setup failed for [rms reference :1-99.N,CA,C,O :1-99.N,CA,O
> out
> > > perresavg.dat]: Skipping
> > >
> > >
> > > --
> > > regards
> > >
> > > Bharat Lakhani
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> regards
>
> Bharat Lakhani
> _______________________________________________
> 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 Wed Jun 24 2015 - 14:30:03 PDT
