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

Vitaly Chaban vvchaban at gmail.com
Thu Jun 26 19:45:37 CEST 2008

> 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'm sure the correct way to fix your problem is to check every
interacting site if it has got that charge it should have got according to
the force field model you currently apply.

You are also advised to consult the original papers which describes
the derivation of the mentioned charges.

Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svobody sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban

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