[gmx-users] non-integer total charge of a Lysine molecule??

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 26 19:50:02 CEST 2008

> My question is... 
> why is the total charge (qtot) of the molecule 0.89 as shown in topol.top above, instead of the
> expected +1?

My guess would be that you chose the wrong options when you ran 
pdb2gmx.  If you were to choose the normal NH3+ and COO- options, you 
will get the wrong charge.  What you want is to choose the 
Zwitterion-NH3+ and Zwitterion-COO- options with pdb2gmx.  Those will 
give the correct atom types and charges for a zwitterionic single amino 


> The gomacs automatically choose opls_283 (atom number 5 in topol.top above) as C-alpha (CA),
> instead of opls_224B, the usual C-alpha for amino acids. If I manually replace CA from opls_283
> (charge=0.04) to opls-224B (charge=0.14), then the total charge improves to be 0.99. Is this the
> correct way to fix the problem of non-integer total charge in this case? If so, is 0.99 for total
> charge close enough to 1 so I can move on to the next stage? 
> I greatly appreciate in advance your kind help and/or advice!
> Regards,
> Sung Hyun
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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