Dear Dr. Daniel and Amber people,
Thanks a lot for your suggestions. Using a combination of parmed.py and
cpptraj have successfully generated the required combined trajectory file.
But I am getting the following error while running clustering on it. Is it
a memory problem? The trajectory size is 3.2 GB. Please suggest.
gm.linux-rfml:~/Documents/MD/1PRG/cluster_1PRG/combined_traj_clustering>
ptraj
../../../100ns_MDoutputfiles/processed_trajs/2Q6S_BVT_VAC_prosparm.prmtop <
combined_traj_cluster.in
\-/
-/- PTRAJ: a utility for processing trajectory files
/-\
\-/ Version: "AMBER 12.0 integrated" (4/2012)
-/- Executable is: "ptraj"
/-\ Running on 1 processor(s)
\-/ Residue labels:
GLU SER ALA ASP LEU ARG ALA LEU ALA LYS
HIE LEU TYR ASP SER TYR ILE LYS SER PHE
PRO LEU THR LYS ALA LYS ALA ARG ALA ILE
LEU THR GLY LYS THR THR ASP LYS SER PRO
PHE VAL ILE TYR ASP MET ASN SER LEU MET
MET GLY GLU ASP LYS ILE LYS PHE LYS HIE
ILE THR PRO LEU GLN GLU GLN SER LYS GLU
VAL ALA ILE ARG ILE PHE GLN GLY CYS GLN
PHE ARG SER VAL GLU ALA VAL GLN GLU ILE
THR GLU TYR ALA LYS SER ILE PRO GLY PHE
VAL ASN LEU ASP LEU ASN ASP GLN VAL THR
LEU LEU LYS TYR GLY VAL HID GLU ILE ILE
TYR THR MET LEU ALA SER LEU MET ASN LYS
ASP GLY VAL LEU ILE SER GLU GLY GLN GLY
PHE MET THR ARG GLU PHE LEU LYS SER LEU
ARG LYS PRO PHE GLY ASP PHE MET GLU PRO
LYS PHE GLU PHE ALA VAL LYS PHE ASN ALA
LEU GLU LEU ASP ASP SER ASP LEU ALA ILE
PHE ILE ALA VAL ILE ILE LEU SER GLY ASP
ARG PRO GLY LEU LEU ASN VAL LYS PRO ILE
GLU ASP ILE GLN ASP ASN LEU LEU GLN ALA
LEU GLU LEU GLN LEU LYS LEU ASN HIE PRO
GLU SER SER GLN LEU PHE ALA LYS LEU LEU
GLN LYS MET THR ASP LEU ARG GLN ILE VAL
THR GLU HID VAL GLN LEU LEU GLN VAL ILE
LYS LYS THR GLU THR ASP MET SER LEU HIE
PRO LEU LEU GLN GLU ILE TYR LYS
PTRAJ: Processing input from "STDIN" ...
PTRAJ: trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/combined_PPARg_traj.mdcrd.gz
Checking coordinates:
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/combined_PPARg_traj.mdcrd.gz
Rank: 0 Atoms: 4367 FrameSize: 106119 TitleSize: 81 NumBox: 0 Seekable 1
PTRAJ: cluster out combtraj_e21 representative pdb average pdb
averagelinkage epsilon 2.1 rms .CA
MASK = .CA
Mask [.CA] represents 268 atoms
[No output trajectory specified (trajout)]
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/combined_PPARg_traj.mdcrd.gz:
90000 frames.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 90000 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File
(/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/combined_PPARg_traj.mdcrd.gz)
is an AMBER trajectory with 90000 sets
NO OUTPUT COORDINATE FILE WAS SPECIFIED
ACTIONS
1> CLUSTERING.
Clusters will be assigned and output to files with the prefix
"combtraj_e21".
The clustering algorithm is AverageLink using RMS as the distance
metric.
Cluster-to-cluster distance is measured by its centroid.
Maximum eccentricity (epsilon) is 2.100000.
The atom selection for best fit is :1-268.CA
Output of type 'all' will be written to a file of type: 'Amber
trajectory'
Output of type 'representative' will be written to a file of type:
'PDB'
Output of type 'average' will be written to a file of type: 'PDB'
Processing AMBER trajectory file
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/combined_PPARg_traj.mdcrd.gz
ERROR in safe_malloc: Error in alloc of 1572120000 bytes
gm.linux-rfml:~/Documents/MD/1PRG/cluster_1PRG/combined_traj_clustering>
*Procedure adopted for combining trajectory:*
gm.linux-rfml:~/Documents/MD/100ns_MDoutputfiles/processed_trajs> cpptraj
-i combined_traj2.in
CPPTRAJ: Trajectory Analysis. V12.5
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from file combined_traj2.in
[parm
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/2Q6S_BVT_VAC_prosparm.prmtop
[BVT]]
[parm
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1PRG_VAC_prosparm.prmtop
[1PRG]]
[parm
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_VAC_prosparm.prmtop
[FGZ]]
[parm
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/2PRG_RGZ_VAC_prosparm.prmtop
[RGZ]]
[parm
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/2XKW_PGZ_A_VAC_prosparm.prmtop
[PGZA]]
[parm
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/2XKW_PGZ_B_VAC_prosparm.prmtop
[PGZB]]
[parm
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/3CDP_YRG_VAC_prosparm.prmtop
[YRG]]
[parm
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/2Q59_M20_VAC_prosparm.prmtop
[M20]]
[parm
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/2PRG_NP1_VAC_prosparm.prmtop
[NP1]]
[parm
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/2PRG_NP2_VAC_prosparm.prmtop
[NP2]]
[parm
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/2PRG_8NA_VAC_prosparm.prmtop
[8NA]]
[parm
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/2Q5P_M24_VAC_prosparm.prmtop
[M24]]
[trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1PRG_prostraj.mdcrd.gz
parm [BVT]]
[1PRG_prostraj.mdcrd.gz] contains 7500 frames.
[trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/2PRG_RGZ_prostraj.mdcrd.gz
parm [BVT]]
[2PRG_RGZ_prostraj.mdcrd.gz] contains 7500 frames.
[trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/2PRG_8NA_prostraj.mdcrd.gz
parm [BVT]]
[2PRG_8NA_prostraj.mdcrd.gz] contains 7500 frames.
[trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/1FM9_FGZ_prostraj.mdcrd.gz
parm [BVT]]
[1FM9_FGZ_prostraj.mdcrd.gz] contains 7500 frames.
[trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/3CDP_YRG_prostraj.mdcrd.gz
parm [BVT]]
[3CDP_YRG_prostraj.mdcrd.gz] contains 7500 frames.
[trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/2XKW_PGZ_B_prostraj.mdcrd.gz
parm [BVT]]
[2XKW_PGZ_B_prostraj.mdcrd.gz] contains 7500 frames.
[trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/2XKW_PGZ_A_prostraj.mdcrd.gz
parm [BVT]]
[2XKW_PGZ_A_prostraj.mdcrd.gz] contains 7500 frames.
[trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/2Q5P_M24_prostraj.mdcrd.gz
parm [BVT]]
[2Q5P_M24_prostraj.mdcrd.gz] contains 7500 frames.
[trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/2PRG_NP1_prostraj.mdcrd.gz
parm [BVT]]
[2PRG_NP1_prostraj.mdcrd.gz] contains 7500 frames.
[trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/2PRG_NP2_prostraj.mdcrd.gz
parm [BVT]]
[2PRG_NP2_prostraj.mdcrd.gz] contains 7500 frames.
[trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/2Q6S_BVT_prostraj.mdcrd.gz
parm [BVT]]
[2Q6S_BVT_prostraj.mdcrd.gz] contains 7500 frames.
[trajin
/home/gm/Documents/MD/100ns_MDoutputfiles/processed_trajs/2Q59_M20_prostraj.mdcrd.gz
parm [BVT]]
[2Q59_M20_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)
[2PRG_RGZ_prostraj.mdcrd.gz] is an AMBER trajectory, Parm 0 (reading 7500
of 7500)
[2PRG_8NA_prostraj.mdcrd.gz] is an AMBER trajectory, Parm 0 (reading 7500
of 7500)
[1FM9_FGZ_prostraj.mdcrd.gz] is an AMBER trajectory, Parm 0 (reading 7500
of 7500)
[3CDP_YRG_prostraj.mdcrd.gz] is an AMBER trajectory, Parm 0 (reading 7500
of 7500)
[2XKW_PGZ_B_prostraj.mdcrd.gz] is an AMBER trajectory, Parm 0 (reading
7500 of 7500)
[2XKW_PGZ_A_prostraj.mdcrd.gz] is an AMBER trajectory, Parm 0 (reading
7500 of 7500)
[2Q5P_M24_prostraj.mdcrd.gz] is an AMBER trajectory, Parm 0 (reading 7500
of 7500)
[2PRG_NP1_prostraj.mdcrd.gz] is an AMBER trajectory, Parm 0 (reading 7500
of 7500)
[2PRG_NP2_prostraj.mdcrd.gz] is an AMBER trajectory, Parm 0 (reading 7500
of 7500)
[2Q6S_BVT_prostraj.mdcrd.gz] is an AMBER trajectory, Parm 0 (reading 7500
of 7500)
[2Q59_M20_prostraj.mdcrd.gz] is an AMBER trajectory, Parm 0 (reading 7500
of 7500)
Coordinate processing will occur on 90000 frames.
PARAMETER FILES:
0: [BVT], 4367 atoms, 268 res, no box, 90000 frames
1: [1PRG], 4367 atoms, 268 res, no box
2: [FGZ], 4367 atoms, 268 res, no box
3: [RGZ], 4367 atoms, 268 res, no box
4: [PGZA], 4367 atoms, 268 res, no box
5: [PGZB], 4367 atoms, 268 res, no box
6: [YRG], 4367 atoms, 268 res, no box
7: [M20], 4367 atoms, 268 res, no box
8: [NP1], 4367 atoms, 268 res, no box
9: [NP2], 4367 atoms, 268 res, no box
10: [8NA], 4367 atoms, 268 res, no box
11: [M24], 4367 atoms, 268 res, no box
REFERENCE COORDS:
No reference coordinates.
No frames defined.
OUTPUT TRAJECTORIES:
[combined_PPARg_traj.mdcrd.gz] is an AMBER trajectory, Parm 0: Writing
90000 frames
ACTIONS: Initializing 0 actions:
BEGIN TRAJECTORY PROCESSING:
.....................................................
PARM [2Q6S_BVT_VAC_prosparm.prmtop]: Setting up 0 actions.
----- [1PRG_prostraj.mdcrd.gz] (1-7500, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- [2PRG_RGZ_prostraj.mdcrd.gz] (1-7500, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- [2PRG_8NA_prostraj.mdcrd.gz] (1-7500, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- [1FM9_FGZ_prostraj.mdcrd.gz] (1-7500, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- [3CDP_YRG_prostraj.mdcrd.gz] (1-7500, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- [2XKW_PGZ_B_prostraj.mdcrd.gz] (1-7500, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- [2XKW_PGZ_A_prostraj.mdcrd.gz] (1-7500, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- [2Q5P_M24_prostraj.mdcrd.gz] (1-7500, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- [2PRG_NP1_prostraj.mdcrd.gz] (1-7500, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- [2PRG_NP2_prostraj.mdcrd.gz] (1-7500, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- [2Q6S_BVT_prostraj.mdcrd.gz] (1-7500, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- [2Q59_M20_prostraj.mdcrd.gz] (1-7500, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 90000 frames and processed 90000 frames.
ACTION OUTPUT:
DATASETS:
There are no data sets set up for analysis.
gm.linux-rfml:~/Documents/MD/100ns_MDoutputfiles/processed_trajs>
On Thu, Mar 21, 2013 at 8:05 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Wed, Mar 20, 2013 at 11:07 PM, Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
> > I have tried your suggestion except upgrading cpptraj (for this I guess I
>
> You should really consider updating and recompiling your AmberTools
> installation. There are bugs in your version of the code (not just in
> cpptraj) that could affect future results. Re-running configure should
> be enough to patch your installation.
>
> > 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.
>
> In cases like these it really helps to take a close look at your
> structure. The problem is that in the 1PRG structure you have a
> C-terminal LEU and an N-terminal GLU, while in the 1FM9 structure you
> have non-terminal versions of these residues (hence the extra atoms).
> Either remove these residues from both structures, or just remove the
> extra terminal atoms in 1PRG.
>
> -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 Tue Mar 26 2013 - 04:30:03 PDT
