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

[chiba.s.ac]

Dear Chris,

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?

Best regards,
Shuntaro.


----- 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?
>> 
>> 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.
>> 
>> 
>> -- 
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the 
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>