[gmx-users] wrong charge assignment(?) on ATP in rtp file
chiba.s.ac at m.titech.ac.jp
Wed Jul 7 20:31:59 CEST 2010
I really appreciate your comment.
> Can you provide a reference for the idea that the charge groups must have integer charge?
I actually do not have any critical literature for the idea of “whole number rule”;
1) In the item of “Charge group” of the “GROMACS USER MANUAL, ver.4” in chapter 3, a charge group is described as follow “A charge group is a small set of nearby atoms with an integer net charge.”
2) So far, I have not seen decimal total group charges.
Hence I had thought that the rule is an algorithm requirement or an empirically obtained criterion or something. It seems that I do not need to care about decimal total group charges as I am planning to use PME.
> Can you find the original reference for the G53a6 ATP parameters?
Unfortunately I could not find the original paper. It is also unavailable who made the parameter when and how. If you have information about the parameters, could you please let me know?
----- Original Message -----
>> From: chris.neale at utoronto.ca
>> To: gmx-users at gromacs.org
>> Date: 2010-07-08 01:46:19
>> Subject: [gmx-users] wrong charge assignment(?) on ATP in rtp file
>> 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,
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