Serious Steric Atom Clashes

From: Nara Dashdorj (dnr_at_physics.purdue.edu)
Date: Sun Oct 23 2005 - 13:45:43 CDT

Dear NAMD Users:

I am simulation this integral membrane protein that has several
prosthetic groups. After equilibrating my solvated model, which
encompasses protein in lipid membrane (~220 000 atoms), I wanted to
release my protein, but encountered the problem of steric clashes of atoms.

I narrowed down my problem by simulating my protein chains separately in
vacuum, which resulted in the conclusion of atoms of heme groups are
clashing with protein subunits. I vissually checked it loading into VMD,
which indicates several residues are really close to the hemes (within
~2 Angstroms). These are not artifact of topology, it is inherent in the
crystal structure (3.0 Angstrom resolution structure).

These clashes cause huge VDW energy, and simulation produces the
following log, in which NAMD restarts conjugate gradient algorithm
repeadetly without any success...

Info: NONZERO IMPRECISION IN COULOMB TABLE: 1.27055e-21 (767)
1.48231e-21 (767)
Info: Entering startup phase 8 with 42778 kB of memory in use.
Info: Finished startup with 94696 kB of memory in use.
TCL: Minimizing for 1000 steps
PRESSURE: 0 nan nan nan nan nan nan nan nan nan
GPRESSURE: 0 nan nan nan nan nan nan nan nan nan
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
TOTAL2 TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG

ENERGY: 0 41796.6193 16153.7223 1893.0569
482.6422 781586.9314 99999999.9999 0.0000
0.0000 0.0000 99999999.9999 0.0000 99999999.9999
99999999.9999 0.0000 -99999999.9999 -99999999.9999
2918023.1080 -99999999.9999 -99999999.9999

INITIAL STEP: 1e-06
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
RESTARTING CONJUGATE GRADIENT ALGORITHM
INITIAL STEP: 2.5e-07
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
RESTARTING CONJUGATE GRADIENT ALGORITHM
INITIAL STEP: 6.25e-08
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
RESTARTING CONJUGATE GRADIENT ALGORITHM
INITIAL STEP: 1.5625e-08
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
RESTARTING CONJUGATE GRADIENT ALGORITHM
INITIAL STEP: 3.90625e-09
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
RESTARTING CONJUGATE GRADIENT ALGORITHM
INITIAL STEP: 9.76562e-10

To resolve this, I played with minimization options such as minBabyStep,
minTinyStep, and maximumMove without any success!

Any ideas to resolve this problem is truly appreciated!

--nd

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