Re: [AMBER] problem combining trajectories with diff. number of residues

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Thu, 21 Mar 2013 10:37:03 +0530

Dear Dr. Daniel and Amber people,
I have tried your suggestion except upgrading cpptraj (for this I guess I
don't have to reinstall/recompile Amber as well, I just need to follow the
procedure for latest AmberTools12 tar file only, is it? please confirm and
suggest).

The old box error is gone, but there is still a miss match with number of
atoms while the number of residues is identical now.
I have attached the two initial two pdb files from which it is clear that
1FM9 had only 1,272 and 273 extra residues. After removing them why number
of atoms is not matching is a question to me? Waters were already stripped
form pdb, prmtops and mdcrd files.
Please suggest how to fix this.

What I did is as follows:

I have stripped ligand and extra terminal residues to write new prmtop for
1FM9 using
gm.linux-rfml:~/Documents/MD/100ns_MDoutputfiles/processed_trajs> parmed.py
Choose an Amber Topology file to load:
../../100ns_MD_inputfiles/1FM9_FGZ_VAC.prmtop
Loaded Amber topology file ../../100ns_MD_inputfiles/1FM9_FGZ_VAC.prmtop

Reading input from STDIN...
> strip :1,272,273 #273 is ligand
  Removing mask ':1,272,273' (108 atoms) from the topology file.

> outparm
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_VAC_prosparm.prmtop
  Outputting Amber topology file
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_VAC_prosparm.prmtop
> quit
Quitting.

Then I used the following commands in cpptraj input file
combined_traj1.in
-----------
parm /home/gm/Documents/MD/100ns_MD_inputfiles/1PRG_VAC.prmtop [1PRG]
parm
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_VAC_prosparm.prmtop
[FGZ]
trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1PRG_prostraj.mdcrd.gz
trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_prostraj.mdcrd.gz
parm [FGZ]
trajout combined_PPARg_traj.mdcrd.gz nobox
------------
gm.linux-rfml:~/Documents/MD/100ns_MDoutputfiles/processed_trajs> cpptraj
-i combined_traj1.in

CPPTRAJ: Trajectory Analysis. V12.1
    ___ ___ ___ ___
     | \/ | \/ | \/ |
    _|_/\_|_/\_|_/\_|_

INPUT: Reading Input from file combined_traj1.in
  [parm /home/gm/Documents/MD/100ns_MD_inputfiles/1PRG_VAC.prmtop [1PRG]]
  [parm
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_VAC_prosparm.prmtop
[FGZ]]
  [trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1PRG_prostraj.mdcrd.gz]
        [1PRG_prostraj.mdcrd.gz] contains 7500 frames.
  [trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_prostraj.mdcrd.gz
parm [FGZ]]
        [1FM9_FGZ_prostraj.mdcrd.gz] contains 7500 frames.
  [trajout combined_PPARg_traj.mdcrd.gz nobox]

INPUT TRAJECTORIES:
  [1PRG_prostraj.mdcrd.gz] is an AMBER trajectory, Parm 0 (reading 7500 of
7500)
  [1FM9_FGZ_prostraj.mdcrd.gz] is an AMBER trajectory, Parm 1 (reading 7500
of 7500)
  Coordinate processing will occur on 15000 frames.

PARAMETER FILES:
 0: [1PRG], 4401 atoms, 270 res, no box, 7500 frames
 1: [FGZ], 4398 atoms, 270 res, no box, 7500 frames

REFERENCE COORDS:
  No reference coordinates.
  No frames defined.

OUTPUT TRAJECTORIES:
  [combined_PPARg_traj.mdcrd.gz] is an AMBER trajectory, Parm 0: Writing
7500 frames

ACTIONS: Initializing 0 actions:
BEGIN TRAJECTORY PROCESSING:
.....................................................
PARM [1PRG_VAC.prmtop]: Setting up 0 actions.
----- [1PRG_prostraj.mdcrd.gz] (1-7500, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

.....................................................
PARM [1FM9_FGZ_VAC_prosparm.prmtop]: Setting up 0 actions.
----- [1FM9_FGZ_prostraj.mdcrd.gz] (1-7500, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 15000 frames and processed 15000 frames.

ACTION OUTPUT:

DATASETS:
  There are no data sets set up for analysis.



On Wed, Mar 20, 2013 at 8:29 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> Hi,
>
> On Tue, Mar 19, 2013 at 1:28 AM, Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
> > CPPTRAJ: Trajectory Analysis. V12.1
>
> You're using an out-of-date version of cpptraj, please update your
> AmberTools installation (cpptraj should be at least 12.5).
>
> > INPUT: Reading Input from file combined_traj1.in
> > [parm /home/gm/Documents/MD/100ns_MD_inputfiles/1PRG_VAC.prmtop [1PRG]]
> > [parm
> /home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_VAC_prosparm.prmtop
> [FGZ]]
> > [trajin
> /home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1PRG_prostraj.mdcrd.gz]
> > [1PRG_prostraj.mdcrd.gz] contains 7500 frames.
> > [trajin
> /home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_prostraj.mdcrd.gz
> [FGZ]]
> > Error in box coord line of trajectory
>
> You are not specifying the parm for the last trajin correctly; it's
> trying to use the first parm ([1PRG]). The correct way to specify
> different topologies with 'trajin' is either 'parm <filename>', 'parm
> <tag>', or 'parmindex <#>', so you need:
>
> trajin
> /home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_prostraj.mdcrd.gz
> parm [FGZ]
>
> However, this still won't fix your issue since cpptraj currently
> checks that an input topology matches the output topology (this
> prevents weird problems with non-matching atom/residue names if you're
> doing e.g. PDB/Mol2 output). So this line:
>
> > [trajout combined_PPARg_traj.mdcrd.gz nobox]
>
> Will only be valid for trajectories associated with the specified
> topology (in this case no topology is specified so it defaults to the
> first one loaded, 1PRG).
>
> I can think of one way to get around this, but you should be VERY VERY
> CAREFUL. Currently the trajectories and topologies are still different
> (# atoms and # residues do not match):
>
> 0: [1PRG], 4401 atoms, 270 res, no box, 7500 frames
> 1: [FGZ], 4468 atoms, 271 res, no box
>
> If you can strip the FGZ topology/coordinates so that the # residues,
> # atoms, and atom ordering EXACTLY match 1PRG, you could use the 1PRG
> topology to read in the stripped FGZ trajectory as well, then trajout
> will work.
>
> Also note that with cpptraj, you can use the 'outprefix <prefix>'
> keyword with 'strip' to generate a topology compatible with the
> stripped trajectory, e.g.:
>
> parm input.parm7
> trajin input.nc
> strip :WAT outprefix nowat
> trajout nowat.input.nc
>
> will generate nowat.input.parm7, which corresponds with nowat.input.nc.
>
> Good luck,
>
> -Dan
>
> --
> -------------------------
> 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.
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, +91-7709129400.
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in




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Received on Wed Mar 20 2013 - 22:30:02 PDT
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