AMBER Archive (2004)

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

From: Yuhui Cheng (amberuser3_at_yahoo.com)
Date: Sun Jul 25 2004 - 21:01:13 CDT

Hi,

   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.

Thanks,
Yuhui

                
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