[gmx-users] Max #atoms in a charge group: 68 > 64

[Samuel Coulbourn Flores 花山]

Hi Guys,

Thanks for past help received on this list.

I am having a problem which I hope I can get some insight on.  I am  
trying to simulate Adenylate Kinase binding substrate analog AP5A  
(from Shapiro et al).  The problem is that this ligand (which is  
basically two Adenosines chained together with five phosphates) is a  
little on the large side, with 68 atoms.  I get the following error on  
trying to run genion:

Max #atoms in a charge group: 68 > 64

Can someone explain  to me how the ligand is different from the  
protein (which certainly has more than 64 atoms!)?  Is the protein not  
considered a charge group?  Can I somehow tell gromacs not treat the  
ligand as something other than a charge group?  Alternatively, can I  
increase the max # atoms in a charge group?  I'm happy to let it run a  
little more slowly if that's the only consequence.

Many thanks

Sam

Samuel Coulbourn Flores
Altman Lab
Department of BioEngineering
Stanford University
samuel.flores at aya.yale.edu
650.644.8416

花山
科学者
生物工学部
スタンフォ一ド大学
スタンフォ一ド、カリフォルニア、米国

















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