Hi,
Pay close attention to any warnings given by cpptraj. In particular you
have several warnings like this:
Warning: Res 1: # atoms in Tgt (22) != # atoms in Ref (14)
Warning: Res 3: # atoms in Tgt (7) != # atoms in Ref (14)
Warning: Res 4: # atoms in Tgt (15) != # atoms in Ref (24)
and so on. The RMSD calculation requires a 1 to 1 correspondence between
target and reference atoms. You may need to adjust range, refrange, and/or
perresmask to get things to line up. For example, to try to line residues
2-30 in the target with 20-48 in the reference and excluding hydrogens from
the per-residue mask,
rmsd :2-30.CA :20-48.CA first perres \
perresout perres.agr range 2-30 refrange 20-48 \
perresmask &!.H=
I recommend consulting the manual to make sure you understand what each
keyword is doing. Good luck,
-Dan
On Wed, Jul 29, 2015 at 8:47 PM, bharat lakhani <lakhbharat.gmail.com>
wrote:
> Dear Dan
>
> After installing cpptraj amber14 version on your recommendation. I am
> running following script to calculate all-atom and per residue rmsd for
> same protein with different numbering system.
>
>
> parm test1.prmtop [test1]
> parm test2.prmtop [test2]
>
>
> trajin test1.pdb parm [test1]
> #trajin test2.pdb parmindex 1
>
> reference test2.pdb parm [test2] [BF]
>
>
> rms :6-115.CA ref [BF] :1-115.CA out rmsd
> rms :6-115.CA ref [BF] :1-115.CA perres perresout rms_vs_time.dat
> perresavg
> perresavg.dat
>
>
> The first all CA atom rmsd seems to be working fine. But all residues rmsd
> does not working at all. Please let me know If i am doing something wrong.
> Enclosed here is cpptraj output file for the reference.
>
> Thanks
>
> On Thu, Jun 25, 2015 at 10:28 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Hi,
> >
> > On Wed, Jun 24, 2015 at 9:52 PM, bharat lakhani <lakhbharat.gmail.com>
> > wrote:
> >
> > >
> > > Warning: Active reference has only 1528 atoms, parm 'StructureA.prmtop'
> > has
> > > 1552
> > >
> > > Warning: Parm will only have reference coordinates for the first 1528
> > atoms
> > > (distance-based masks only)
> > >
> >
> > As the warning states, this is only an issue if you are using
> > distance-based masks (which I don't think you are). Are there other error
> > messages?
> >
> > -Dan
> >
> >
> > >
> > >
> > >
> > > On Wed, Jun 24, 2015 at 11:02 PM, Daniel Roe <daniel.r.roe.gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > It's always best to use the latest version (15). There have been many
> > > > improvements and fixes to cpptraj in particular since Amber 12.
> > > >
> > > > -Dan
> > > >
> > > > On Wednesday, June 24, 2015, bharat lakhani <lakhbharat.gmail.com>
> > > wrote:
> > > >
> > > > > Thanks for your help. Currently I am using Amer12. does cpptraj has
> > > been
> > > > > update in the recent version and I should switch to Amber15?
> > > > > Sincerel
> > > > >
> > > > > On Wed, Jun 24, 2015 at 5:01 PM, Daniel Roe <
> daniel.r.roe.gmail.com
> > > > > <javascript:;>> wrote:
> > > > >
> > > > > > 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
> > > > > <javascript:;>>
> > > > > > 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
> > > > > <javascript:;>>
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Hi,
> > > > > > > >
> > > > > > > > On Wed, Jun 24, 2015 at 11:56 AM, bharat lakhani <
> > > > > lakhbharat.gmail.com <javascript:;>
> > > > > > >
> > > > > > > > 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 <javascript:;>
> > > > > > > > > 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 <javascript:;>
> > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > regards
> > > > > > >
> > > > > > > Bharat Lakhani
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
> > > > > > > AMBER.ambermd.org <javascript:;>
> > > > > > > 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 <javascript:;>
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > regards
> > > > >
> > > > > Bharat Lakhani
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org <javascript:;>
> > > > > 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)
> > _______________________________________________
> > 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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 30 2015 - 08:30:03 PDT
