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

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jul 7 21:35:42 CEST 2010


The parameters for ATP (and several other building blocks and
molecules) in the GROMOS 53a5 and 53a6 force fields are, AFAIK,
inherited from the older versions, albeit with some modifications to
bring them in line with the rest of the force field. So they weren't
reparameterized and thus do not exactly follow the philosophy of the
force field. The parameters for ATP are likely more in line with the
GROMOS 43a5 force field. Maybe that would be a better choice.



On Wed, Jul 7, 2010 at 8:35 PM,  <chris.neale at utoronto.ca> wrote:
> "It seems that I do not need to care about decimal total group charges as I
> am planning to use PME."
> -- well, find it in the literature first!
> -- original message --
> 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 $B!H (Bwhole
> number rule $B!I (B;
> 1) In the item of  $B!H (BCharge group $B!I (B of the  $B!H (BGROMACS USER
> MANUAL, ver.4 $B!I (B in chapter 3, a charge group is described as follow
>  $B!H (BA charge group is a small set of nearby atoms with an integer net
> charge. $B!I (B
> 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.
> --
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

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