[gmx-users] Charge assignment

Justin A. Lemkul jalemkul at vt.edu
Thu May 20 13:38:59 CEST 2010

Michael McGovern wrote:
> Hi everyone.
>   I'm working on getting parameters for a protein system that has some 
> linker residues in it.  These linkers are nothing too strange, they just 
> have some amine groups.  I can get bonded parameters from the prodrg 
> server.  I know the charge groups are unreliable.  I'm using the 53A6 
> parameter set, and I read how the charges there were derived.  They 
> specifically did the iteration of parameters manually to give the same 
> charges for the same functional groups.  Does this mean I can take 
> charges from the same functional groups in the rtp files for amino acids 
> and use those charges in my linkers?  If it is necessary to validate, 
> should that be done on the linkers as molecules in their acidic, 
> unlinked form?  
> Thanks everyone.

Generally, the functional groups in the GROMOS parameter sets are very 
transferrable, as their derivation scheme would suggest.  I suppose about the 
only validation you could do would be to prove that the properties of your 
linker molecules (whatever they may be) are reproduced by the application of 
these parameters when not joined to your protein.  Reproduction of 
condensed-phase behavior and thermodynamic properties was the goal of the GROMOS 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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