AMBER Archive (2002)

Subject: amber7, gaff and minimization (fwd)

From: amber_at_heimdal.compchem.ucsf.edu
Date: Mon Aug 26 2002 - 16:50:50 CDT

---------- Forwarded message ----------
Date: Thu, 22 Aug 2002 11:20:56 -0700 (PDT)
From: Prabal Maiti <maiti_at_wag.caltech.edu>
To: AMBER mailing list <amber_at_heimdal.compchem.ucsf.edu>
Subject: amber7, gaff and minimization (fwd)

I am trying to do minimization with explicit water for a protonated
polymer with Cl- ions/ For the polymer I am using gaff.dat ff
parameters. I have created appropiate lib file for the protonated polymer
which xleap can read. With xleap added Cl- and TIP3P water. When I do
minimization nothing happens in the sense that energy (or RMS) does not
change after 100 steps of minimiation. Same thing continues for 3000 steps
of conjugate gradient minimization.
Can someone point out what is going wrong.

Thanks
Prabal

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 -1.1146E+04 1.5028E+01 1.3618E+02 N_3 79

 BOND = 5.7138 ANGLE = 341.1777 DIHED =
30.4355
 VDWAALS = 1343.9347 EEL = -12948.8915 HBOND =
0.0000
 1-4 VDW = 6.9355 1-4 EEL = 74.2945 RESTRAINT =
0.0000
  
  NSTEP ENERGY RMS GMAX NAME NUMBER
    100 -1.2042E+04 1.3444E+01 4.2349E+01 HC 85

 BOND = 1.4934 ANGLE = 77.5862 DIHED =
36.7561
 VDWAALS = 701.1367 EEL = -12921.8617 HBOND =
0.0000
 1-4 VDW = 8.9152 1-4 EEL = 53.7126 RESTRAINT =
0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
    200 -1.2042E+04 1.3444E+01 4.2349E+01 HC 85

 BOND = 1.4934 ANGLE = 77.5860 DIHED =
36.7561
 VDWAALS = 701.1337 EEL = -12921.8556 HBOND =
0.0000
 1-4 VDW = 8.9151 1-4 EEL = 53.7124 RESTRAINT =
0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
    300 -1.2042E+04 1.3444E+01 4.2349E+01 HC 85

 BOND = 1.4933 ANGLE = 77.5858 DIHED =
36.7561
 VDWAALS = 701.1307 EEL = -12921.8494 HBOND =
0.0000
 1-4 VDW = 8.9151 1-4 EEL = 53.7122 RESTRAINT =
0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
    400 -1.2042E+04 1.3444E+01 4.2350E+01 HC 85

 BOND = 1.4933 ANGLE = 77.5856 DIHED =
36.7561
 VDWAALS = 701.1277 EEL = -12921.8432 HBOND =
0.0000
 1-4 VDW = 8.9151 1-4 EEL = 53.7120 RESTRAINT =
0.0000 

-- 
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Prabal K Maiti                             Email:maiti_at_wag.caltech.edu
Beckman Institute (139-74)                       pkmaiti_at_yahoo.com
California Institute of Technology         Tel:626-395-8151 (O)
400 South Wilson Avenue                       :626-744-1363 (H)                    
Pasadena, CA 91125                         Fax:626-585-0918
                                           Home add: 110 S. Michigan Ave.
http://www.wag.caltech.edu/home/maiti      Apt # 19, Pasadena, CA 91106
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