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
Received on Tue Dec 04 2012 - 10:00:02 PST
