solvate using Helmut Grubmuller's SOLVATE and then VMD, then how to minimize properly!

From: ydhuang2727 (ydhuang2727_at_163.com)
Date: Tue Nov 11 2008 - 02:30:40 CST

Hi, everyone !
 I use Helmut Grubmuller's SOLVATE
(http://www.mpibpc.mpg.de/home/grubmueller/downloads/solvate/index.html)
to generate a closely contoured solvent bubble around the solute, and
then use VMD solvate to get the final cube°£
But when i run NAMD, some odd results in .log file generates as follows:
Warning: DUPLICATE BOND ENTRY FOR ht-ht
PREVIOUS VALUES k=0 x0=1.514
   USING VALUES k=0 x0=1.5139
Warning: DUPLICATE vdW ENTRY FOR OT
PREVIOUS VALUES sigma=3.1506 epsilon=0.1521 sigma14=3.1506 epsilon14=0.1521
   USING VALUES sigma=2.8509 epsilon=0.1591 sigma14=2.8509 epsilon14=0.1591
Warning: DUPLICATE vdW ENTRY FOR HT
PREVIOUS VALUES sigma=0.4 epsilon=0.046 sigma14=0.4 epsilon14=0.046
   USING VALUES sigma=1.4254 epsilon=0.0498 sigma14=1.4254 epsilon14=0.0498
Warning: DUPLICATE vdW ENTRY FOR CA
PREVIOUS VALUES sigma=3.5501 epsilon=0.07 sigma14=3.5501 epsilon14=0.07
   USING VALUES sigma=3.517 epsilon=0.01 sigma14=3.517 epsilon14=0.01
Warning: DUPLICATE vdW ENTRY FOR FE
PREVIOUS VALUES sigma=1.1582 epsilon=1e-04 sigma14=1.1582 epsilon14=1e-04
   USING VALUES sigma=2.27 epsilon=0.01 sigma14=2.27 epsilon14=0.01
Warning: DUPLICATE vdW ENTRY FOR ZN
PREVIOUS VALUES sigma=1.9422 epsilon=0.25 sigma14=1.9422 epsilon14=0.25
   USING VALUES sigma=2.484 epsilon=0.01 sigma14=2.484 epsilon14=0.01
OPENING EXTENDED SYSTEM TRAJECTORY FILE
INITIAL STEP: 1e-06
GRADIENT TOLERANCE: nan
BRACKET: 0 nan nan nan nan
RESTARTING CONJUGATE GRADIENT ALGORITHM
INITIAL STEP: 5e-07
GRADIENT TOLERANCE: nan
BRACKET: 0 nan nan nan nan
RESTARTING CONJUGATE GRADIENT ALGORITHM
INITIAL STEP: 2.5e-07
GRADIENT TOLERANCE: nan
BRACKET: 0 nan nan nan nan
NEW SEARCH DIRECTION
INITIAL STEP: 1.25e-07
GRADIENT TOLERANCE: nan
BRACKET: 0 nan nan nan nan
NEW SEARCH DIRECTION
thanks very much!

Dong
 

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