From: Hugh Heldenbrand (helde010_at_umn.edu)
Date: Tue Jun 08 2010 - 10:30:41 CDT
Hello-
I am a new user of namd. I compiled the 2010-06-07 nightly build for
the first time yesterday. I compiled (on an amd64 system) charm-6.1.3
using the intel compiler version 11.1 and ompi version 1.4.1. I
compiled namd using the same intel compiler. I successfully ran the
apoa1 test.
Now I am trying to run a simulation of a system that I have set up using
AMBER's parmeter/coordinate generating utilities with namd. I am using
the TIP4PEW water model. namd bombs with the following error message:
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : WATER
Info: ERROR TOLERANCE : 0.0005
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED 1276007367
Info: USE HYDROGEN BONDS? NO
Info: Using AMBER format force field!
Info: AMBER PARM FILE ./namd_data/2OUE.parm7
Info: COORDINATE PDB ./namd_data/2OUE_eq81.pdb
Info: Exclusions will be read from PARM file!
Info: SCNB (VDW SCALING) 2
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Reading parm file (./namd_data/2OUE.parm7) ...
PARM file in AMBER 7 format
Warning: Encounter 10-12 H-bond term
Warning: CORRECTION OF ZERO MASS ATOMS TURNED OFF BECAUSE LONE PAIRS ARE
USED
Warning: Found 11254 H-H bonds.
FATAL ERROR: Failed to find water bond lengths
[0] Stack Traceback:
[0] _Z8namd_diePKc+0x72 [0x4d8922]
[1] _ZN8Molecule17build_atom_statusEv+0x28de [0x90175e]
[2] _ZN8Molecule9read_parmEP4parm+0x1ab7 [0x8fed67]
[3] _ZN8MoleculeC1EP13SimParametersP10ParametersP4parm+0x22a [0x8fd18a]
[4] _ZN9namdState14configListInitEP10ConfigList+0xf32 [0x918d12]
[5] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x40b [0x98a04b]
[6] TclInvokeStringCommand+0x91 [0xb45078]
[7] /home/bc2/heldenbr/namd/namd_CVS_Source/Linux-x86_64-icc/namd2
[0xb7aec8]
[8] Tcl_EvalEx+0x176 [0xb7b50b]
[9] Tcl_EvalFile+0x134 [0xb72f14]
[10] _ZN9ScriptTcl3runEPc+0x13 [0x988a03]
[11] main+0x26a [0x4dd2fa]
[12] __libc_start_main+0xea [0x2a964ebaaa]
[13] _ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_c+0x3a
[0x4d822a]
I am not sure what to include from my input file. Some relevant options
that I am using might be:
waterModel tip4
rigidBonds water
amber on
useGroupPressure yes
If necessary, I can try to put my input files in their entirety online.
I should note that in addition to the problem reading my water model, I
don't think that the warning about encountering a 10-12 term is correct,
the forcefield that I am using does not include those terms (maybe it
encountered one that was 0?)
Any ideas? Thanks in advance.
-Hugh Heldenbrand
Dept. of Chemistry,
U of MN
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