AMBER: anion and cation simulaton

From: gurpreet singh <>
Date: Tue, 25 Mar 2008 21:52:29 +0530

Respected users,

 I am using amber 9 for an anion (PF6) and equal number of cation
simulation. After some steps, some of P-F bonds were not visible when seen
in softwares like VMD. Probable reason for this would be the increase of
the P-F distance more than the optimum distance or more than the max limit
defined in VMD.

To prevent this ,We tried keeping distance and angle restraints on all P-F
bonds, even then very large energy values were observed. For reference part
of output file is shown below

   1000 1.3575E+04 4.0955E-01 9.4143E+00 F3 935

 BOND = 69.3525 *ANGLE = 28352.4129* DIHED =
 VDWAALS = -2025.1706 EEL = -10418.9524 HBOND =
 1-4 VDW = 214.8050 1-4 EEL = -3930.3295 RESTRAINT =
 EAMBER = 13014.7433

In the initial steps of the simulation we used antchamber for generating the
prep file, since antechamber is not suitable for most of the inorganics like
this, we had to use '-j 5" which means the atom and part bond type as atom
and bond type prediction index. Although I think the above mention problem
is not at all related to this antechamber issue still just to remove the
doubt I am providing this information.

My other question ; can we do this type of simulations using Amber force


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Received on Fri Apr 18 2008 - 21:13:57 PDT
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