parthi...@ncbs.res.in wrote:
Hi
I am using a dimer for my simulation system which is connected by 2
disulfide bonds.
After energy minimization for even few cycles, the disulfide bond breaks
which is not expected.
Bonds do not break in classical molecular mechanics. One of two things is
happening:
1. There was never a bond to begin with (check your topology)
2. The bond is highly strained, in which case something is wrong with your
structure.
i have applied amber99 force field and prepared the system. while i tried
with another force field in Gromacs which did not worked at all.
What does that mean? What failed?
also i have tried by editing specbond.dat as well but of no use.
In what way? Have you seen the information at:
http://www.gromacs.org/Documentation/File_Formats/specbond.dat
-Justin
can any one share/discuss some ideas how to fix this.
reg's,
Parthiban.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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