Hi, I have 2*4 GB = 8 GB RAM, so that is surprising as to why its not able
to find 1.5GB?
On Tue, Mar 26, 2013 at 8:25 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
>
--
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
Received on Tue Mar 26 2013 - 20:30:02 PDT
