AMBER: about the parameter of the cystein pair in MD simulation

From: Yuhui Cheng <>
Date: Sun, 25 Jul 2004 19:01:13 -0700 (PDT)


   When I use "CYX" to describle CYS-CYS pair in my
research project, the S-S bond always was broken even
in my gradually equilibrium process. The distance
between S-S can enlarge from 2.0 A to 3.0 A in the
water box and above 3.0 A in the gas phase. I checked
my topolgy file, the residue name is CYX and sulfer
type is "S", and I used parm99, which specified the
distance of S-S is 2.038 A. When I check another
collegue's MD trajectory, it has the same problem.


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Received on Mon Jul 26 2004 - 03:53:00 PDT
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