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)
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Received on Tue Dec 04 2012 - 14:30:02 PST
