Thanks. I will keep this in mind for future use.
On Wed, Dec 5, 2012 at 3:38 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> This is OK, except your trajin statments should have a 'parm' keyword
> before the parm tag, e.g.
>
> trajin
> /windows/D/Users/gncp/Documents/RGZ_2cluster/RGZ_epsilon21/RGZ_e21.c0
> parm [RGZ]
>
> In this case it happens to be OK since 'trajin' will default to the
> first parm read in, which happens to be the one you want.
>
> -Dan
>
> On Tue, Dec 4, 2012 at 10:30 AM, Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
> > Dear Dr. Daniel R. Roe,
> > thanks for the detailed explanation.
> > Please let me know if my cpptraj input file.given below has problems. I
> > seems to have worked well.
> >
> > On Tue, Dec 4, 2012 at 10:47 PM, Vaibhav Dixit <vaibhavadixit.gmail.com
> >wrote:
> >
> >> Dear Dr. Jason and other Amber users,
> >> I finally understood the correct usage from the manual. Can you please
> >> confirm if my following cpptraj input is meaningful or not?
> >> I got meaningful results, but just want to confirm my usage of the
> >> keywords and commands.
> >> Thanks.
> >>
> >> cpptraj input file.
> >> ----
> >> parm
> >>
> /home/gncp/Documents/MD/PPAR_MD_study/100ns_MD_inputfiles/2PRG_RGZ_VAC.prmtop
> >> [RGZ]
> >> trajin
> >> /windows/D/Users/gncp/Documents/RGZ_2cluster/RGZ_epsilon21/RGZ_e21.c0
> [RGZ]
> >> parm /home/gncp/Documents/MD/PPAR_MD_study/1PRG/1PRG_VAC.prmtop
> [1PRG_VAC]
> >> reference 1PRG_e21.rep.c0.inpcrd parm [1PRG_VAC] [struct0]
> >> rmsd :1-270.CA,C,N ref [struct0] :1-270.CA,C,N out 1PRG_r0_RGZ_r0.rmsd
> >>
> >> trajin
> >> /windows/D/Users/gncp/Documents/RGZ_2cluster/RGZ_epsilon21/RGZ_e21.c1
> [RGZ]
> >> rmsd :1-270.CA,C,N ref [struct0] :1-270.CA,C,N out 1PRG_r0_RGZ_r1.rmsd
> >>
> >> trajin
> >> /windows/D/Users/gncp/Documents/RGZ_2cluster/RGZ_epsilon21/RGZ_e21.c0
> [RGZ]
> >> reference 1PRG_e21.rep.c1.inpcrd parm [1PRG_VAC] [struct1]
> >> rmsd :1-270.CA,C,N ref [struct1] :1-270.CA,C,N out 1PRG_r1_RGZ_r0.rmsd
> >>
> >> trajin
> >> /windows/D/Users/gncp/Documents/RGZ_2cluster/RGZ_epsilon21/RGZ_e21.c1
> [RGZ]
> >> rmsd :1-270.CA,C,N ref [struct1] :1-270.CA,C,N out 1PRG_r1_RGZ_r1.rmsd
> >> ---------
> >>
> >>
> >> On Mon, Dec 3, 2012 at 10:26 PM, Vaibhav Dixit <vaibhavadixit.gmail.com
> >wrote:
> >>
> >>> Thanks Jason,
> >>> I tried to make right input files, but could not understand the usage
> >>> given in AmberTools12 (page 193) clearly.
> >>>
> >>> I tried following input for cpptraj
> >>>
> >>> cpptraj_1PRG_RGZ_trail.in
> >>> ------------
> >>> trajin
> >>> /windows/D/Users/gncp/Documents/RGZ_2cluster/RGZ_epsilon21/RGZ_e21.c0
> >>> parm /home/gncp/Documents/MD/PPAR_MD_study/1PRG/1PRG_VAC.prmtop
> >>> reference 1PRG_e21.rep.c0.inpcrd [struct0]
> >>> rmsd BB :1-270.CA,C,N ref [struct0] :1-270.CA,C,N out
> 1PRG_r0_RGZ_r0.rmsd
> >>>
> >>> trajin
> >>> /windows/D/Users/gncp/Documents/RGZ_2cluster/RGZ_epsilon21/RGZ_e21.c1
> >>> parm /home/gncp/Documents/MD/PPAR_MD_study/1PRG/1PRG_VAC.prmtop
> >>> reference 1PRG_e21.rep.c0.inpcrd [struct0]
> >>> rmsd BB :1-270.CA,C,N ref [struct0] :1-270.CA,C,N out
> 1PRG_r0_RGZ_r1.rmsd
> >>> ------------
> >>>
> >>> and got the following message from cpptraj. Please help me understand
> why
> >>> it could not pick the right prmtop and use only residues 1-270 for rmsd
> >>> analysis from both trajectory and reference inpcrd files.
> >>>
> >>> --------------
> >>> linux-hb9b:/home/gncp/Documents/MD/PPAR_MD_study/1PRG/rmsd_1PRG #
> cpptraj
> >>>
> /home/gncp/Documents/MD/PPAR_MD_study/100ns_MD_inputfiles/2PRG_RGZ_VAC.prmtop
> >>> < cpptraj_1PRG_RGZ_trail.in
> >>>
> >>> CPPTRAJ: Trajectory Analysis. V12.4
> >>> ___ ___ ___ ___
> >>> | \/ | \/ | \/ |
> >>> _|_/\_|_/\_|_/\_|_
> >>>
> >>> INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit:
> >>> > [trajin
> >>> /windows/D/Users/gncp/Documents/RGZ_2cluster/RGZ_epsilon21/RGZ_e21.c0]
> >>> [RGZ_e21.c0] contains 5876 frames.
> >>> > [parm /home/gncp/Documents/MD/PPAR_MD_study/1PRG/1PRG_VAC.prmtop]
> >>> > [reference 1PRG_e21.rep.c0.inpcrd [struct0]]
> >>> Error: Number of atoms in Amber Restart 1PRG_e21.rep.c0.inpcrd (4401)
> >>> does not
> >>> match number in associated parmtop (4466)
> >>> Error: Could not set up 1PRG_e21.rep.c0.inpcrd for reading.
> >>> Error: reference: Could not set up trajectory.
> >>> > [rmsd BB :1-270.CA,C,N ref [struct0] :1-270.CA,C,N out
> >>> 1PRG_r0_RGZ_r0.rmsd]
> >>> > [trajin
> >>> /windows/D/Users/gncp/Documents/RGZ_2cluster/RGZ_epsilon21/RGZ_e21.c1]
> >>> [RGZ_e21.c1] contains 1624 frames.
> >>> > [parm /home/gncp/Documents/MD/PPAR_MD_study/1PRG/1PRG_VAC.prmtop]
> >>> Warning: Parm
> >>> /home/gncp/Documents/MD/PPAR_MD_study/1PRG/1PRG_VAC.prmtop already
> loaded,
> >>> skipping.
> >>> > [reference 1PRG_e21.rep.c0.inpcrd [struct0]]
> >>> Error: Number of atoms in Amber Restart 1PRG_e21.rep.c0.inpcrd (4401)
> >>> does not
> >>> match number in associated parmtop (4466)
> >>> Error: Could not set up 1PRG_e21.rep.c0.inpcrd for reading.
> >>> Error: reference: Could not set up trajectory.
> >>> > [rmsd BB :1-270.CA,C,N ref [struct0] :1-270.CA,C,N out
> >>> 1PRG_r0_RGZ_r1.rmsd]
> >>> >
> >>> INPUT TRAJECTORIES:
> >>> [RGZ_e21.c0] is an AMBER trajectory, Parm 0 (reading 5876 of 5876)
> >>> [RGZ_e21.c1] is an AMBER trajectory, Parm 0 (reading 1624 of 1624)
> >>> Coordinate processing will occur on 7500 frames.
> >>>
> >>> PARAMETER FILES:
> >>> 0:
> >>>
> /home/gncp/Documents/MD/PPAR_MD_study/100ns_MD_inputfiles/2PRG_RGZ_VAC.prmtop,
> >>> 4466 atoms, 272 res, no box, 7500 frames
> >>> 1: /home/gncp/Documents/MD/PPAR_MD_study/1PRG/1PRG_VAC.prmtop, 4401
> >>> atoms, 270 res, no box
> >>>
> >>> REFERENCE COORDS:
> >>> No reference coordinates.
> >>> No frames defined.
> >>>
> >>> OUTPUT TRAJECTORIES:
> >>> No files.
> >>>
> >>> ACTIONS: Initializing 2 actions:
> >>> 0: [rmsd BB :1-270.CA,C,N ref [struct0] :1-270.CA,C,N out
> >>> 1PRG_r0_RGZ_r0.rmsd]
> >>> Error: Rmsd::init: Could not get reference index -1
> >>> Error: Init failed for [rmsd BB :1-270.CA,C,N ref [struct0] :1-270.CA
> ,C,N
> >>> out 1PRG_r0_RGZ_r0.rmsd].
> >>> --
> >>>
> >>> On Mon, Dec 3, 2012 at 8:23 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
> >>>
> >>>> cpptraj was designed specifically for this task. You can load
> structures
> >>>> with different topologies and calculate RMSDs between 'different'
> >>>> structures (as long as the selection in both structures have the same
> #
> >>>> of
> >>>> atoms).
> >>>>
> >>>> Look at the manual for cpptraj to learn how to use it.
> >>>>
> >>>> Good luck,
> >>>> Jason
> >>>>
> >>>> On Mon, Dec 3, 2012 at 9:25 AM, Vaibhav Dixit <
> vaibhavadixit.gmail.com
> >>>> >wrote:
> >>>>
> >>>> > Dear Monica,
> >>>> > Waters and ions are already removed from the trajectory, so they are
> >>>> not
> >>>> > the source of problem here.
> >>>> > I must emphasize that, I want to plot rmsd for the trajectory with
> >>>> > reference to a structure (PDB) which has one residue less than those
> >>>> > present in the MD trajectory.
> >>>> > This is causing ptraj warning for mismatch in number of atoms.
> >>>> >
> >>>> > On Mon, Dec 3, 2012 at 6:02 PM, <monica.imtech.res.in> wrote:
> >>>> >
> >>>> > > Hi
> >>>> > > I guess ypu can remove water and other ions etc.from the prmtop
> >>>> file and
> >>>> > > then
> >>>> > > try one more time for rmsd calculation by ptraj coz atom number
> >>>> > difference
> >>>> > > can
> >>>> > > be due to this.
> >>>> > >
> >>>> > > Thanx
> >>>> > > monica
> >>>> > >
> >>>> > >
> >>>> > > > Dear Amber community members,
> >>>> > > > I have trajectory files for a protein generated from different
> PDB
> >>>> > files
> >>>> > > > with different number of residues.
> >>>> > > > For e.g. I have structure 1PRG with residues 1-270 and 2PRG with
> >>>> > residues
> >>>> > > > 1-271 (272 is ligand).
> >>>> > > >
> >>>> > > > Now I want to plot rmsd between trajectory of 2PRG and reference
> >>>> > > structure
> >>>> > > > (PDB generate with ambpdb) of 1PRG.
> >>>> > > > I am following the below mentioned procedure, but I'm not sure
> if
> >>>> the
> >>>> > > > results are meaningful (rmsd > 500 ?). Ptraj also gives warning
> >>>> that
> >>>> > > > expected and actual number of atoms are different.
> >>>> > > >
> >>>> > > > *Please suggest me how can I use two prmtop for different
> >>>> trajectories
> >>>> > > > together to get the rmsd between two trajectories of same
> protein
> >>>> but
> >>>> > > with
> >>>> > > > different number of residues (hence different sequence).*
> >>>> > > >
> >>>> > > > Step 1. ptraj 2PRG.prmtop < 2PRG_new_traj.in
> >>>> > > >
> >>>> > > > ptraj input file for step 1.
> >>>> > > > 2PRG_new_traj.in
> >>>> > > > ------------
> >>>> > > > trajin 2PRG.mdcrd
> >>>> > > > strip :271
> >>>> > > > trajout 2PRG_new.mdcrd
> >>>> > > > -----------
> >>>> > > >
> >>>> > > > Step 2. Then I have generated prmtop for 2PRG with residue 271
> >>>> deleted
> >>>> > > > (2PRG_new.prmtop)
> >>>> > > >
> >>>> > > > Step 3. ptraj 2PRG_new.prmtop < 2PRG_1PRG.in
> >>>> > > >
> >>>> > > > ptraj input file for step 3.
> >>>> > > > 2PRG_1PRG.in
> >>>> > > > ---------
> >>>> > > > trajin 2PRG_new.mdcrd
> >>>> > > > rms reference 1PRG.pdb out 2PRG_1PRG.rmsd :1-271.CA,C,N,O
> >>>> > > > --------
> >>>> > > >
> >>>> > > >
> >>>> > > > --
> >>>> > > > With regards
> >>>> > > >
> >>>> > > > Vaibhav A. Dixit
> >>>> > > > Ph.D. Scholar
> >>>> > > > Department of Medicinal Chemistry
> >>>> > > > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> >>>> > > > Sector 67, Phase X, S.A.S. Nagar (Mohali)
> >>>> > > > Punjab -160 062 INDIA
> >>>> > > > Phone (Mobile): +919915214408
> >>>> > > > E-mail: vaibhavadixit.gmail.com
> >>>> > > > www.niper.nic.in
> >>>> > > > _______________________________________________
> >>>> > > > AMBER mailing list
> >>>> > > > AMBER.ambermd.org
> >>>> > > > http://lists.ambermd.org/mailman/listinfo/amber
> >>>> > > >
> >>>> > >
> >>>> > >
> >>>> > >
> >>>> ______________________________________________________________________
> >>>> > > सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान
> परिषद)
> >>>> > > Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF
> >>>> CSIR)
> >>>> > > सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
> >>>> > > पिन कोड/PIN CODE :160036
> >>>> > > दूरभाष/EPABX :0172 6665 201-202
> >>>> > >
> >>>> > > _______________________________________________
> >>>> > > AMBER mailing list
> >>>> > > AMBER.ambermd.org
> >>>> > > http://lists.ambermd.org/mailman/listinfo/amber
> >>>> > >
> >>>> >
> >>>> >
> >>>> >
> >>>> > --
> >>>> > With regards
> >>>> >
> >>>> > Vaibhav A. Dixit
> >>>> > Ph.D. Scholar
> >>>> > Department of Medicinal Chemistry
> >>>> > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> >>>> > Sector 67, Phase X, S.A.S. Nagar (Mohali)
> >>>> > Punjab -160 062 INDIA
> >>>> > Phone (Mobile): +919915214408
> >>>> > E-mail: vaibhavadixit.gmail.com
> >>>> > www.niper.nic.in
> >>>> > _______________________________________________
> >>>> > AMBER mailing list
> >>>> > AMBER.ambermd.org
> >>>> > http://lists.ambermd.org/mailman/listinfo/amber
> >>>> >
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Jason M. Swails
> >>>> Quantum Theory Project,
> >>>> University of Florida
> >>>> Ph.D. Candidate
> >>>> 352-392-4032
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> With regards
> >>>
> >>> Vaibhav A. Dixit
> >>> Ph.D. Scholar
> >>> Department of Medicinal Chemistry
> >>> Natl. Inst. Pharm. Edu. & Res. (NIPER)
> >>> Sector 67, Phase X, S.A.S. Nagar (Mohali)
> >>> Punjab -160 062 INDIA
> >>> Phone (Mobile): +919915214408
> >>> E-mail: vaibhavadixit.gmail.com
> >>> www.niper.nic.in
> >>>
> >>
> >>
> >>
> >> --
> >> With regards
> >>
> >> Vaibhav A. Dixit
> >> Ph.D. Scholar
> >> Department of Medicinal Chemistry
> >> Natl. Inst. Pharm. Edu. & Res. (NIPER)
> >> Sector 67, Phase X, S.A.S. Nagar (Mohali)
> >> Punjab -160 062 INDIA
> >> Phone (Mobile): +919915214408
> >> E-mail: vaibhavadixit.gmail.com
> >> www.niper.nic.in
> >>
> >
> >
> >
> > --
> > With regards
> >
> > Vaibhav A. Dixit
> > Ph.D. Scholar
> > Department of Medicinal Chemistry
> > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> > Sector 67, Phase X, S.A.S. Nagar (Mohali)
> > Punjab -160 062 INDIA
> > Phone (Mobile): +919915214408
> > E-mail: vaibhavadixit.gmail.com
> > www.niper.nic.in
> > _______________________________________________
> > 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 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Tue Dec 04 2012 - 19:30:02 PST
