Hi,
It could be a memory error. The 'malloc' call is trying to allocate
~1.5 GB (in addition to any other memory that may be in use) - do you
have that much memory available?
-Dan
On Tue, Mar 26, 2013 at 5:11 AM, Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
> 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
> _______________________________________________
> 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 Mar 26 2013 - 08:00:06 PDT
