Re: xMDFF: model file is not given

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Fri May 25 2018 - 10:31:56 CDT

Something is going wrong during the map generation step. My first
suggestion is to try using a newer version of vmd (at least 1.9.3). It's
been a while, but if I remember correctly, I believe there were some
changes to xMDFF between 1.9.2 and 1.9.3 to work with newer versions of
phenix.

On Fri, May 25, 2018 at 8:05 AM Antonio Vila Sanjurjo <anton.vila_at_udc.es>
wrote:

> 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/
> <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/
> <http://www.ks.uiuc.edu/Research/vmd/>*
> *Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> <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--00000000000083e60d056d0978e7--

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