[AMBER] AM1/D - ATP+PROTEIN

From: Fernando Martín García <fmgarcia.cbm.uam.es>
Date: Fri, 25 May 2012 12:22:47 +0200

 Hello,

 I'm working with AM1/d, trying to perform the reaction in a ATPase.
 Everything works fine if I only include ATP and catalytic water in QM
 part and also if I add some residues. The problem start when I add a
 salt-brige (E-R) to QM part. In that case, the geometry of QM part
 breaks. The extra point is that if I only include the salt-bridge, QM
 geometry works fine.

 Has anybody the any idea where it could be the problem? Has anybody
 experience with AM1/d and ATPases to give some clue?

 Thanks.

 est regards, 

-- 
 ==============================================
  Fernando Martín García
  Molecular Modelling Group - Lab 312.1
  Molecular Biology Center "Severo Ochoa"
  C/ NICOLáS CABRERA, 5.
  UAM University. Cantoblanco, 28049 Madrid. Spain.
  TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
  Web: http://fertoledo.wordpress.com/
 ==============================================
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Received on Fri May 25 2012 - 03:30:02 PDT
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