[gmx-users] wrong charge assignment(?) on ATP in rtp file

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Jul 7 18:46:19 CEST 2010

Dear Shuntaro:

If you're using PME then there is no need to have unit charge in  
charge groups. I can't comment on any other errors that may or may not  
be in that topology as I have never simulated ATP. Also, if you're not  
using PME, then I can not advise you if it is ok to have non-integer  
charge groups. Can you provide a reference for the idea that the  
charge groups must have integer charge? Can you find the original  
reference for the G53a6 ATP parameters?


-- original message --

Dear gmxusers,

I am going to carry out an MD simulation using G53a6 FF, whose system  
contains some ATP molecules.  In order to know whether the calculation  
is possible or not, I looked for a topology of ATP in ffG53a6.rtp.   
Although the topology exists, each total charge of charge group 9, 10  
and 11 is not a whole number (-0.925,?-0.925 and -1.15 respectively).   
It seems to be wrong.

My questions are as follows:
1) How can I fix them, otherwise can I get the appropriate topology.
2) There are not only ATP but many residues which are not listed in  
the original paper of G53a5/6 ?23 (13) 1656-1676, Journal of  
Computational Chemistry?.  How were these parameters derived??Is it  
consistent with the method described in the paper, i.e. are charges  
fitted to reproduce the corresponding experimental value?

I really appreciate all of replies.

Best regards,

More information about the gromacs.org_gmx-users mailing list