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?
Chris.
-- 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,
Shuntaro.
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