Hi All,
Last week I sent the question below but got no reply. So I'm asking a rather general question.
What is the best way to run simulation of a protein having Zinc ions coordinated to CYS and HIS resiudes?
Any pointers to the parameters would be helpful.
Thanks,
Manish
From: manish.datt.hotmail.com
To: amber.ambermd.org
Subject: Leap error with Zinc ions
Date: Thu, 14 Apr 2011 10:22:29 -0400
Hi All,
I trying to prepare a system with protein having tetrahedrally coordinated zinc ions. I using the cationic dummy atom approach. But I getting following error in Leap:
ERROR: Comparing atoms
.R<CYM 261>.A<SG 8>,
.R<CYM 263>.A<SG 8>,
.R<CYM 264>.A<SG 8>, and
.R<CYM 265>.A<SG 8>
to atoms
.R<ZNB 270>.A<D2 3>,
.R<ZNB 270>.A<D1 2>,
.R<ZNB 270>.A<D3 4>, and
.R<CYM 261>.A<SG 8>
This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 140
!FATAL: Message: Atom named D2 from ZNB did not match !
!
!ABORTING.
Complete Leap log and pdb files are attached
Please help me solve this problem.
Thanks,
Manish
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Received on Mon Apr 18 2011 - 08:00:02 PDT
