Hi,
When you are loading in a trajectory, you need to specify which parm
file it will use if it's not the first parm loaded. For example, lets
say I want to load in a trajectory of a 5000 atom structure, and a
reference with 200 atoms:
parm protein.5000atom.parm7
trajin protein.5000atom.mdcrd
parm ref.200atom.parm7
reference ref.200atom.rst7 parm ref.200atom.parm7
Since no parm/parmindex keyword is given to the 'trajin
protein.5000atom.mdcrd' command, it uses the first parm loaded by
default (protein.5000atom.parm7 in this case). In the 'reference
ref.200atom.rst7' command the 'parm ref.200atom.parm7' keyword is
given, specifying that this structure should use a previously loaded
parm with filename 'ref.200atom.parm7'. The 'parmindex 1' keyword
would work as well (parm indices start from 0). To simplify tracking
of parm/reference files (e.g. if your parm file name is really long),
you can use 'tags'. For example:
parm protein.5000atom.parm7
trajin protein.5000atom.mdcrd
parm ref.200atom.parm7 [ref2parm]
reference ref.200atom.rst7 parm [ref2parm] [ref2]
rms :1-12.CA ref [ref2] :
1-12.CA out rmsd.dat
In this case I apply the tag [ref2parm] to 'ref.200atom.parm7', which
I can then use with the 'parm' keyword in the 'reference' statement in
place of the filename. I also give the reference structure a tag
[ref2] which I then use in the following 'rms' command.
Hopefully this clears things up - if you still have questions let me know.
-Dan
On Mon, Dec 3, 2012 at 9:56 AM, 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
> _______________________________________________
> 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
Received on Tue Dec 04 2012 - 09:30:03 PST
