About the err of "Constraint failure"

From: Aurum Bai (javacfish_at_yahoo.com.cn)
Date: Sun Feb 21 2010 - 03:13:25 CST

Dear all,

I follow the FEP/TI's tutorial to do mutate the amino acid.
I use this script for constructing ACE-ALA-Y2A-ALA-CT3 as below:

***********************************
topology ../common/top_all22_prot.inp
topology tyr2ala.top
segment Y2A {
first none
last none
pdb tyr2ala.pdb }
patch ACE Y2A:1
patch CT3 Y2A:1
coordpdb tyr2ala.pdb Y2A
writepsf setup.psf
writepdb setup.pdb
*************************************

The final structure of molecule is right, but when I run the simulation of minize and following equilibrate, the errs happen:

"ERROR: Constraint failure in RATTLE algorithm for atom 44!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
====================================================

What is wrong with it? and how do solve it?

Thanks very much!

javacfish

      

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