xMDFF: model file is not given

From: Antonio Vila Sanjurjo (anton.vila_at_udc.es)
Date: Fri May 25 2018 - 07:00:32 CDT

Hi,

while running namd to perform xMDFF refinement I got the following error

[ulcbmavs_at_c7257 xMDFF]$ namd2 Frpa_righ-seq_modrefine_refine_2_051518-step1.namd
Charm++: standalone mode (not using charmrun)
Charm++> Running in SMP mode: numNodes 1, 1 worker threads per process
Charm++> The comm. thread both sends and receives messages
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Converse/Charm++ Commit ID: v6.7.1-0-gbdf6a1b-namd-charm-6.7.1-build-2016-Nov-07-136676
Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'.
Charm++> scheduler running in netpoll mode.
Charm++ communication thread will sleep due to single-process run.
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (24-way SMP).
Charm++> cpu topology info is gathered in 0.001 seconds.
Info: Built with CUDA version 8000
Did not find +devices i,j,k,... argument, using all
Pe 0 physical rank 0 binding to CUDA device 0 on c7257: 'Tesla K80' Mem: 11439MB Rev: 3.7
Info: NAMD 2.12 for Linux-x86_64-verbs-smp-CUDA
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60701 for verbs-linux-x86_64-ifort-smp-icc
Info: Built Mér Out 11 10:29:34 CEST 2017 by software on c7257
Info: 1 NAMD 2.12 Linux-x86_64-verbs-smp-CUDA 1 c7257 ulcbmavs
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 11.4987 s
CkLoopLib is used in SMP with a simple dynamic scheduling (converse-level notification) but not using node-level queue
Info: 267.488 MB of memory in use based on /proc/self/stat
Info: Configuration file is Frpa_righ-seq_modrefine_refine_2_051518-step1.namd
Info: Working in the current directory /mnt/netapp1/Store_ulcbmavs/xMDFF
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 20
Info: LOAD BALANCER Centralized
Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
Info: LDB PERIOD 4000 steps
Info: FIRST LDB TIMESTEP 100
Info: LAST LDB TIMESTEP -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: MIN ATOMS PER PATCH 40
Info: INITIAL TEMPERATURE 300
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 80
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME Frpa_righ-seq_modrefine_refine_2_051518-step1.dcd
Info: DCD FREQUENCY 1000
Info: DCD FIRST STEP 1000
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME Frpa_righ-seq_modrefine_refine_2_051518-step1
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME Frpa_righ-seq_modrefine_refine_2_051518-step1.restart
Info: RESTART FREQUENCY 1000
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON 9
Info: SWITCHING OFF 10
Info: PAIRLIST DISTANCE 11
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: PAIRLISTS ENABLED
Info: MARGIN 0
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 13.5
Info: ENERGY OUTPUT STEPS 100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000
Info: PRESSURE OUTPUT STEPS 100
Info: GRID FORCE ACTIVE
Info: Please include this reference in published work using
Info: the Gridforce module of NAMD: David Wells, Volha Abramkina,
Info: and Aleksei Aksimentiev, J. Chem. Phys. 127:125101-10 (2007).
Info: MGRIDFORCE key 0
Info: Potfile step1.dx
Info: Scale 0.1 0.1 0.1
Info: File Frpa_righ-seq_modrefine_refine_cagrid_051518.pdb
Info: Col O
Info: ChargeCol B
Info: VOffset 0 0 0
Info: Continuous K1 FALSE
Info: Continuous K2 FALSE
Info: Continuous K3 FALSE
Info: Volts FALSE
Info: Gridforce-Lite FALSE
Info: Gridforce-CheckSize TRUE
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 300
Info: LANGEVIN USING BBK INTEGRATOR
Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : WATER
Info: ERROR TOLERANCE : 1e-08
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: NONBONDED FORCES EVALUATED EVERY 2 STEPS
Info: RANDOM NUMBER SEED 1527006160
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB Frpa_righ-seq_modrefine_refine_2_autopsf.pdb
Info: STRUCTURE FILE Frpa_righ-seq_modrefine_refine_2_autopsf.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS par_all36_prot.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 132 BONDS
Info: 362 ANGLES
Info: 702 DIHEDRAL
Info: 35 IMPROPER
Info: 6 CROSSTERM
Info: 53 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PSF FILE: 0.140646
Info: READING EXTRA BONDS FILE Frpa_righ-seq_modrefine_refine_2_extrabonds-051518.txt
Info: READING EXTRA BONDS FILE Frpa_righ-seq_modrefine_refine_2-extrabonds-cispeptide_051518.txt
Info: READING EXTRA BONDS FILE Frpa_righ-seq_modrefine_refine_2-extrabonds-chirality_051518.txt
Info: READ 98 EXTRA BONDS
Info: READ 98 EXTRA ANGLES
Info: READ 1131 EXTRA DIHEDRALS
Info: READ 1140 EXTRA IMPROPERS
Info: Reading pdb file Frpa_righ-seq_modrefine_refine_2_autopsf.pdb
Info: TIME FOR READING PDB FILE: 0.00873685
Info:
Command = zcat step1.dx.Z
Filename.Z = step1.dx.Z
Command = gzip -d -c step1.dx.gz
Filename.gz = step1.dx.gz
FATAL ERROR: Problem reading grid force potential file
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Problem reading grid force potential file

[0] Stack Traceback:
[0:0] CmiAbortHelper+0x56 [0x1420a36]
[0:1] _Z8NAMD_diePKc+0x9d [0x6f842d]
[0:2] _ZN21GridforceFullMainGrid10initializeEPcP13SimParametersP16MGridforceParamsi+0x2922 [0xf5c792]
[0:3] [0xf4dd66]
[0:4] _ZN8Molecule22build_gridforce_paramsEP10StringListS1_S1_S1_P3PDBPc+0x7c6 [0xfe7426]
[0:5] [0x102e044]
[0:6] _ZN9NamdState14configListInitEP10ConfigList+0x348 [0x1032378]
[0:7] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0xc2 [0x1169c82]
[0:8] TclInvokeStringCommand+0x88 [0x1693678]
[0:9] [0x1696190]
[0:10] [0x16d8f73]
[0:11] [0x16ded33]
[0:12] TclEvalObjEx+0x86 [0x1697de6]
[0:13] [0x16a0d3d]
[0:14] [0x1696190]
[0:15] [0x1697576]
[0:16] Tcl_EvalEx+0x16 [0x1697d56]
[0:17] Tcl_FSEvalFileEx+0x151 [0x16f9b61]
[0:18] [0x16a6d4a]
[0:19] [0x1696190]
[0:20] [0x1697576]
[0:21] Tcl_EvalEx+0x16 [0x1697d56]
[0:22] Tcl_FSEvalFileEx+0x151 [0x16f9b61]
[0:23] Tcl_EvalFile+0x2e [0x16f9d1e]
[0:24] _ZN9ScriptTcl4loadEPc+0x10 [0x11662b0]
[0:25] main+0x460 [0x716280]
[0:26] __libc_start_main+0xfd [0x7ff161b80d5d]
[0:27] [0x60a769]
Charm++ fatal error:
FATAL ERROR: Problem reading grid force potential file

[0] Stack Traceback:
[0:0] LrtsAbort+0x431 [0x14208f1]
[0:1] _Z8NAMD_diePKc+0x9d [0x6f842d]
[0:2] _ZN21GridforceFullMainGrid10initializeEPcP13SimParametersP16MGridforceParamsi+0x2922 [0xf5c792]
[0:3] [0xf4dd66]
[0:4] _ZN8Molecule22build_gridforce_paramsEP10StringListS1_S1_S1_P3PDBPc+0x7c6 [0xfe7426]
[0:5] [0x102e044]
[0:6] _ZN9NamdState14configListInitEP10ConfigList+0x348 [0x1032378]
[0:7] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0xc2 [0x1169c82]
[0:8] TclInvokeStringCommand+0x88 [0x1693678]
[0:9] [0x1696190]
[0:10] [0x16d8f73]
[0:11] [0x16ded33]
[0:12] TclEvalObjEx+0x86 [0x1697de6]
[0:13] [0x16a0d3d]
[0:14] [0x1696190]
[0:15] [0x1697576]
[0:16] Tcl_EvalEx+0x16 [0x1697d56]
[0:17] Tcl_FSEvalFileEx+0x151 [0x16f9b61]
[0:18] [0x16a6d4a]
[0:19] [0x1696190]
[0:20] [0x1697576]
[0:21] Tcl_EvalEx+0x16 [0x1697d56]
[0:22] Tcl_FSEvalFileEx+0x151 [0x16f9b61]
[0:23] Tcl_EvalFile+0x2e [0x16f9d1e]
[0:24] _ZN9ScriptTcl4loadEPc+0x10 [0x11662b0]
[0:25] main+0x460 [0x716280]
[0:26] __libc_start_main+0xfd [0x7ff161b80d5d]
[0:27] [0x60a769]
Aborted

this is the content of map.log

Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 24 CPUs detected.
Info) Free system memory: 105386MB (81%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 1 available CUDA accelerator:
Info) [0] Tesla K80 13 SM_3.7 @ 0.82 GHz, 11GB RAM, AE2, ZCP
Info) Dynamically loaded 2 plugins in directory:
Info) /opt/cesga/vmd/1.9.2/lib/plugins/LINUXAMD64/molfile
0.4
Frpa_righ-seq_modrefine_refine_2_autopsf.psf Frpa_righ-seq_modrefine_refine_2_autopsf.pdb step1.dx all_scaled2.mtz 0 0 0 5 5 {noh and not water} 0
Frpa_righ-seq_modrefine_refine_2_autopsf.psf
Frpa_righ-seq_modrefine_refine_2_autopsf.pdb
step1.dx
all_scaled2.mtz
0
0
0
5
5
noh and not water
0
psfplugin) Detected a Charmm PSF file
Info) Using plugin psf for structure file Frpa_righ-seq_modrefine_refine_2_autopsf.psf
Info) Analyzing structure ...
Info) Atoms: 8255
Info) Bonds: 8346
Info) Angles: 14954 Dihedrals: 21954 Impropers: 1479 Cross-terms: 540
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 542
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 1 Nucleic: 0
0
Info) Using plugin pdb for coordinates from file Frpa_righ-seq_modrefine_refine_2_autopsf.pdb
Info) Finished with coordinate file Frpa_righ-seq_modrefine_refine_2_autopsf.pdb.
0
atomselect0
Info) Opened coordinate file mapinput.pdb for writing.
Info) Finished with coordinate file mapinput.pdb.
computing density map...

phenix.maps: a command line tool to compute various maps and save them in most
of known formats.

How to run the command line version:

1. Run phenix.maps without any arguments: just type phenix.maps in the command
line and hit Enter. This will creare a parameter file called maps.params,
which can be renamed if desired.

2. Edit maps.params file to specify input/output file names, data labels and
the desired maps. It is possible to request as many maps as desired. By
default, the file maps.params specifies 5 maps to be created: 2mFo-DFc,
2mFo-DFc with missing Fobs filled with DFcalc, mFo-DFc and anomalous
difference maps will be output in MTZ format, and one 2mFo-DFc map will be
output in CCP4 format.
NOTE: the anomalous difference map will only be created if the input
reflection data file contains Bijvoet maps (F+/F- or I+/I-).

3. Run this command to compute requested maps: phenix.maps maps.params

Alternately, you may specify input files (and additional parameters) directly
on the command line:

% phenix.maps model.pdb data.mtz

and it will automatically generate the default maps as described above.

Important Facts:

- phenix.maps is available in PHENIX GUI.

- The scope of parameters 'map_coefficients' defines the map that will be
output as Fourier map coefficients. The scope of parameters 'map' defines
the maps that will be output as CCP4 or X-plor format.

- To create several maps: duplicate either 'map_coefficients' or 'map' or both
scopes of parameters as many times as many maps is desired. Then edit each
of them to define the maps.

- A map is defined by specifying a map type using 'map_type' keyword available
within each scope of parameters: 'map_coefficients' or 'map'. The general
supported format for 'map_type' is: [p][m]Fo+[q][D]Fc[_filled]. For
example: 2Fo-Fc, 2mFobs-DFcalc, 3Fobs-2Fmodel, Fo-Fc, mfobs-Dfcalc, anom,
llg. The 'map_type' parser will automatically recognize which map is
requested.

- The program creates as many files with CCP4 or X-plor formatted maps as
is requested, and it creates only one MTZ formatted file with
all Fourier map coefficients in it.

- The CCP4 or X-plor formatted maps can be computed in the entire unit cell
or around selected atoms only.

- Twinning (if detected) will be accounted for automatically. This can be
disabled by using "skip_twin_detection=True" keyword.

- All arrays used in map calculation, for example: Fobs, Fmodel, Fcalc, Fmask,
m, D, etc., can be output into a CNS or MTZ formatted reflection file.

- For those who likes to experiment: bulk solvent correction and anisotropic
scaling can be turned off, the data can be filtered by sigma and resolution.

- For some map types certain 'map_coefficients' or 'map' scope parameters may
not be applicable. For example, for "map_type=anomalous" the keywords
"fill_missing_f_obs" and some other are not applicable.

- For LLG map calculation, if you specify the wavelength any existing heavy
atoms (P or heavier) will be modeled as anomalous scatterers using the
theoretical values of f' and f''.

-------------------------------------------------------------------------------
No map input specified - using default map types
Sorry: model file is not given: maps.input.pdb_file_name=None is not a file
Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
Info) Exiting normally.
vmd >

I cannot understand what I'm doing wrong.

best,

Antón

-- 
-- 
-- 
Antón Vila-Sanjurjo 
Departamento de Bioloxía Celular e Molecular 
Facultade de Ciencias 
Universidade de A Coruña (UDC) 
Campus Zapateira, s/n 
15.071 - A Coruña - España (Spain). 
tlf: (34) 981-167000 ext:2659 
email: anton.vila_at_udc.es 

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