VMD-L Mailing List

From: snoze pa (snoze.pa_at_gmail.com)
Date: Sun Feb 14 2010 - 12:47:04 CST

VMD uses standard amino acid topology and parameter file. You have to
correct your topology file and parameter file based on heme
coordination information.

On Sun, Feb 14, 2010 at 11:32 AM, Francesco Pietra
<chiendarret_at_gmail.com> wrote:
> I came now across a post on charmm forum, telling that in VMD 1.8.3
> the top file about heme is wrong, giving origin to the same error that
> I encountered (if it is really the same!). Is that an issue also for
> VMD 1.8.7 that I used? Unfortunately, the replacement top offered on
> the charmm forum (and which fixed the issue)
>
> there is something wrong with the heme atom types; go to my web page
> and get the c31b1 release of the toppar files and use those. note that
> the heme parameters are in the stream subdirectory (see the first post
> of this discussion for details).
> http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm
> alex
>
> Indeed, that fixed it. Apparently the topology file included with VMD
> 1.8.3 distribution was corrupted.
> Thanks.
> Ralph
>
>
> can't any more be reached.
>
> francesco
>
> On Sun, Feb 14, 2010 at 5:26 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>> Hi:
>> I am trying to minimize a file containing heme, getting error CAN'T
>> FIND BOND PARAMETERS FOR BOND C - CPB IN PARAMETER FILES, as below in
>> full. Actually, there is no C atom in heme, and in my file it is only
>> for residue CO, as follows from the psf file (sorry for the incorrect
>> colums; unable to get plain text in gmail):
>>
>>    2532 O1   154  HEME O2D  OC    -0.760000       15.9990           0
>>    2533 O1   155  CO   C    CM     0.021000       12.0110           0
>>    2534 O1   155  CO   O    OM    -0.021000       15.9990           0
>>
>> I am using VMD 1.8.7 and namd2.7b2
>>
>> francesco_at_tya64:~/$ charmrun $NAMD_HOME/bin/namd2 ++local +p4
>> ++verbose min-01.conf 2&1 | tee min-01.log
>> [1] 3973
>> bash: 1: command not found
>> Charmrun> charmrun started...
>> Charmrun> adding client 0: "127.0.0.1", IP:127.0.0.1
>> Charmrun> adding client 1: "127.0.0.1", IP:127.0.0.1
>> Charmrun> adding client 2: "127.0.0.1", IP:127.0.0.1
>> Charmrun> adding client 3: "127.0.0.1", IP:127.0.0.1
>> Charmrun> Charmrun = 127.0.0.1, port = 43261
>> Charmrun> start 0 node program on localhost.
>> Charmrun> start 1 node program on localhost.
>> Charmrun> start 2 node program on localhost.
>> francesco_at_tya64:~/work_myo/md$ Charmrun> start 3 node program on localhost.
>> Charmrun> node programs all started
>> Charmrun> Waiting for 0-th client to connect.
>> Charmrun> Waiting for 1-th client to connect.
>> Charmrun> client 1 connected (IP=127.0.0.1 data_port=42210)
>> Charmrun> client 2 connected (IP=127.0.0.1 data_port=38956)
>> Charmrun> Waiting for 2-th client to connect.
>> Charmrun> client 3 connected (IP=127.0.0.1 data_port=35927)
>> Charmrun> Waiting for 3-th client to connect.
>> Charmrun> client 0 connected (IP=127.0.0.1 data_port=36170)
>> Charmrun> All clients connected.
>> Charmrun> IP tables sent.
>> Charmrun> node programs all connected
>> Charm++> cpu topology info is being gathered.
>> Charm++> Running on 1 unique compute nodes (4-way SMP).
>> Info: NAMD 2.7b2 for Linux-x86_64
>> Info:
>> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
>> Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
>> 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 60103 for net-linux-x86_64-iccstatic
>> Info: Built Thu Nov 12 22:12:21 CST 2009 by jim on belfast.ks.uiuc.edu
>> Info: 1 NAMD  2.7b2  Linux-x86_64  4    tya64  francesco
>> Info: Running on 4 processors.
>> Info: CPU topology information available.
>> Info: Charm++/Converse parallel runtime startup completed at 0.0138831 s
>> Info: 1.63664 MB of memory in use based on CmiMemoryUsage
>> Info: Found 2 config files.
>> Info: Configuration file is min-01.conf
>> TCL: Suspending until startup complete.
>> Info: SIMULATION PARAMETERS:
>> Info: TIMESTEP               2
>> Info: NUMBER OF STEPS        0
>> Info: STEPS PER CYCLE        20
>> Info: PERIODIC CELL BASIS 1  75 0 0
>> Info: PERIODIC CELL BASIS 2  0 66 0
>> Info: PERIODIC CELL BASIS 3  0 0 69
>> Info: PERIODIC CELL CENTER   14.0475 20.5256 8.67652
>> Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
>> Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
>> Info: LOAD BALANCE STRATEGY  New Load Balancers -- ASB
>> 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: PME BACKGROUND SCALING 1
>> Info: MAX SELF PARTITIONS    20
>> Info: MAX PAIR PARTITIONS    8
>> Info: SELF PARTITION ATOMS   154
>> Info: SELF2 PARTITION ATOMS   154
>> Info: PAIR PARTITION ATOMS   318
>> Info: PAIR2 PARTITION ATOMS  637
>> Info: MIN ATOMS PER PATCH    100
>> Info: INITIAL TEMPERATURE    310
>> Info: CENTER OF MASS MOVING INITIALLY? NO
>> Info: DIELECTRIC             1
>> Info: EXCLUDE                SCALED ONE-FOUR
>> Info: 1-4 SCALE FACTOR       1
>> Info: DCD FILENAME           /home/francesco/work_myo/md/min-01.dcd
>> Info: DCD FREQUENCY          100
>> Info: DCD FIRST STEP         100
>> Info: DCD FILE WILL CONTAIN UNIT CELL DATA
>> Info: XST FILENAME           /home/francesco/work_myo/md/min-01.xst
>> Info: XST FREQUENCY          100
>> Info: NO VELOCITY DCD OUTPUT
>> Info: OUTPUT FILENAME        /home/francesco/work_myo/md/min-01
>> Info: RESTART FILENAME       /home/francesco/work_myo/md/min-01.restart
>> Info: RESTART FREQUENCY      100
>> Info: BINARY RESTART FILES WILL BE USED
>> Info: SWITCHING ACTIVE
>> Info: SWITCHING ON           10
>> Info: SWITCHING OFF          12
>> Info: PAIRLIST DISTANCE      13.5
>> 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                 5
>> Info: HYDROGEN GROUP CUTOFF  2.5
>> Info: PATCH DIMENSION        21
>> Info: ENERGY OUTPUT STEPS    50
>> Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
>> Info: TIMING OUTPUT STEPS    100
>> Info: PRESSURE OUTPUT STEPS  50
>> Info: FIXED ATOMS ACTIVE
>> Info: FORCES BETWEEN FIXED ATOMS ARE CALCULATED
>> Info: LANGEVIN DYNAMICS ACTIVE
>> Info: LANGEVIN TEMPERATURE   310
>> Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
>> Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
>> Info: VELOCITY REASSIGNMENT FREQ  500
>> Info: VELOCITY REASSIGNMENT TEMP  10
>> Info: VELOCITY REASSIGNMENT INCR  10
>> Info: VELOCITY REASSIGNMENT HOLD  310
>> Info: PARTICLE MESH EWALD (PME) ACTIVE
>> Info: PME TOLERANCE               1e-06
>> Info: PME EWALD COEFFICIENT       0.257952
>> Info: PME INTERPOLATION ORDER     4
>> Info: PME GRID DIMENSIONS         80 70 95
>> Info: PME MAXIMUM GRID SPACING    1.5
>> Info: Attempting to read FFTW data from FFTW_NAMD_2.7b2_Linux-x86_64.txt
>> Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
>> Info: Writing FFTW data to FFTW_NAMD_2.7b2_Linux-x86_64.txt
>> Info: FULL ELECTROSTATIC EVALUATION FREQUENCY      2
>> 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 : ALL
>> Info:         ERROR TOLERANCE : 1e-08
>> Info:          MAX ITERATIONS : 100
>> Info: RIGID WATER USING SETTLE ALGORITHM
>> Info: RANDOM NUMBER SEED     12349
>> Info: USE HYDROGEN BONDS?    NO
>> Info: COORDINATE PDB         /home/francesco/work_myo/md/myo-CO-W-ions.pdb
>> Info: STRUCTURE FILE         /home/francesco/work_myo/md/myo-CO-W-ions.psf
>> Info: PARAMETER file: CHARMM format!
>> Info: PARAMETERS
>> /usr/local/lib/vmd/plugins/noarch/tcl/readcharmmpar1.1/par_all27_prot_lipid_na.inp
>> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
>>
>> Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2
>> PREVIOUS VALUES  k=130  theta0=107.5 k_ub=0 r_ub=0
>>   USING VALUES  k=130  theta0=107 k_ub=0 r_ub=0
>> Info: SUMMARY OF PARAMETERS:
>> Info: 307 BONDS
>> Info: 769 ANGLES
>> Info: 1254 DIHEDRAL
>> Info: 81 IMPROPER
>> Info: 6 CROSSTERM
>> Info: 190 VDW
>> Info: 0 VDW_PAIRS
>> FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND C - CPB IN PARAMETER FILES
>> ------------- Processor 0 Exiting: Called CmiAbort ------------
>> Reason: FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND C - CPB IN
>> PARAMETER FILES
>>
>> [0] Stack Traceback:
>>  [0] CmiAbort+0x7f  [0xab6a31]
>>  [1] _Z8NAMD_diePKc+0x62  [0x5093f2]
>>  [2] _ZN10Parameters17assign_bond_indexEPcS0_P4bond+0xfd  [0x925f75]
>>  [3] _ZN8Molecule10read_bondsEP8_IO_FILEP10Parameters+0x177  [0x8e4ceb]
>>  [4] _ZN8Molecule13read_psf_fileEPcP10Parameters+0x35b  [0x8e1aab]
>>  [5] _ZN8MoleculeC9EP13SimParametersP10ParametersPcP10ConfigList+0x259
>>  [0x8e1661]
>>  [6] _ZN8MoleculeC1EP13SimParametersP10ParametersPcP10ConfigList+0x6  [0x8e56ea]
>>  [7] _ZN9NamdState14configListInitEP10ConfigList+0x8e2  [0x90b87c]
>>  [8] _ZN9ScriptTcl9initcheckEv+0x5e  [0x975570]
>>  [9] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x20  [0x97212c]
>>  [10] TclInvokeStringCommand+0x91  [0xae11d8]
>>  [11] TclExecuteByteCode+0x856  [0xafbabf]
>>  [12] Tcl_EvalObjEx+0x2bb  [0xae1beb]
>>  [13] Tcl_IfObjCmd+0x1be  [0xae80be]
>>  [14] /usr/local/namd_2.7b2/bin/namd2 [0xb17028]
>>  [15] Tcl_EvalEx+0x176  [0xb1766b]
>>  [16] Tcl_EvalFile+0x134  [0xb0f074]
>>  [17] _ZN9ScriptTcl4loadEPc+0x10  [0x971612]
>>  [18] _Z18after_backend_initiPPc+0x239  [0x50dc19]
>>  [19] main+0x3a  [0x50d9aa]
>>  [20] __libc_start_main+0xe6  [0x7f852597c1a6]
>>  [21] _ZNSt8ios_base4InitD1Ev+0x52  [0x508d5a]
>> Fatal error on PE 0> FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND
>> C - CPB IN PARAMETER FILES
>>
>> francesco_at_tya64:~/$
>>
>> Thanks for help
>>
>> francesco pietra
>>
>>
>
>