[AMBER] Help needed regarding simulating Lipopolysaccharide

From: Mrinda Jones <mrindajones.gmail.com>
Date: Mon, 17 Aug 2015 16:11:39 +0530

Hi everyone,

I am trying to simulate the Lipopolysaccharide molecule of 271 atoms. The
initial structure was drawn and saved in the .pdb format which stays as the
input file for the simulation (attached herewith).

However when I am trying to run minimization of the water molecules
restraining the molecule itself, it is showing me the output where some
energy values are ************ .

*Min_restraint.input*
Minimization
&cntrl
imin=1,
maxcyc=5000,
ncyc=2500,
ntb=1,
cut=10.0,
igb=0,
ntpr=500,
ntr=1,
ntwx=500,
ntwr=500,
ntwx=500,
ntx=1,
/
Hold solute fixed
100.0
RES 0
END
END

*OUTPUT looks like:*

 NSTEP ENERGY RMS GMAX NAME NUMBER
      1 3.3697E+09 5.9152E+08 5.8990E+10 O2 165

 BOND = 159074.4906 ANGLE = 910.3529 DIHED =
110.2631
 VDWAALS = ************* EEL = -42313.7223 HBOND =
0.0000
 1-4 VDW = 29.5015 1-4 EEL = -709.5993 RESTRAINT =
0.0000


   NSTEP ENERGY RMS GMAX NAME NUMBER
    500 -5.9632E+07 2.2187E+11 2.1625E+13 O2 165

 BOND = 2881.1840 ANGLE = 506.6092 DIHED =
130.4780
 VDWAALS = 4325.9416 EEL = -52240.1784 HBOND =
0.0000
 1-4 VDW = 146.6732 1-4 EEL = ************* RESTRAINT =
0.0000


   NSTEP ENERGY RMS GMAX NAME NUMBER
   1000 -1.1216E+07 7.7985E+09 7.6011E+11 O2 165

 BOND = 2881.1838 ANGLE = 506.6089 DIHED =
130.4780
 VDWAALS = 4325.9416 EEL = -52240.1784 HBOND =
0.0000
 1-4 VDW = 146.6732 1-4 EEL = ************* RESTRAINT =
0.0000



Q1. What could be the error causing this?

Q2. How can I refine it to get a good minimized structure for the next
steps of simulations?



Any suggestions and help would be highly appreciated.

Thanks.
Regards,
M.Jones


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Received on Mon Aug 17 2015 - 04:00:03 PDT
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