[gmx-users] Re:Umbrella sampling of phosphate ion binding (Dallas Warren)

[Justin A. Lemkul]

lloyd riggs wrote:
> Thank you for the advice Dr. Warren,
> 
> I often find the same problem with charges and parameters, and have pulled
> some from the web in some instances.  I have an old CRC book with tables when
> in doubt,
> 
> But I wounder if anyone is interested in just making a tabulation, or wiki
> site to deposite these things when found, as often I feel there would be no
> references of the sources especially if pulled off of the web (although most
> parameters can be found in the gromacs entries), but there exist a large
> amount of difference if people are into accuracy from standardized/averidged
> to individual molecules (such as C with 3 bonds but 90 Vs 110 degree angles,
> and differences in charge due to atoms 2-3 bonds downstream or more for
> larger metals) but I have found these only vary in the 0.00X range usualy,
> but sometimes an order of magnitude more (just from looking).
> 
> I do wounder though about this;
> 
> I have used the PRODRG site a few times with compounds that change only a few
> atoms say on the oposite side of a molecule with 25-30 atoms, and found
> sometimes I get an .itp file with 0.000 charge for say an NH2 (all 3 atoms),
> and the charges of 0.076, -0.019 the next, then 0.03 and -0.007 the next and
> often woundered why?
> 

PRODRG purports to simply look up charges from a library of functional groups, 
but I cannot see any evidence for this case, since quite often (as you note) the 
charges change dramatically.  The net effect is poor results in the simulation 
that uses these topologies.  See our paper:

http://pubs.acs.org/doi/abs/10.1021/ci100335w

There were a number of problems related to amines in PRODRG topologies.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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