[AMBER] Leap error with Zinc ions

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From: Manish Datt <manish.datt.hotmail.com>
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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chemical/x-pdb attachment: zinc2.pdb

text/plain attachment: leap.log

Received on Thu Apr 14 2011 - 07:30:03 PDT