[gmx-users] ions for minimization

Ruben Martinez Buey ruben at akilonia.cib.csic.es
Tue Apr 27 16:11:01 CEST 2004

Hi all,

I want to energy minimize a structure (two proteins + 4 ligands) in a
water box (dodecahedron). The total charge is not 0. what should I do
- add the ions I need to avoid this charge.
- add as negative ions as positive charges I have (Asn, Gln in the
protein and positive charges in the ligands) and as positive ions as
negative charges (Glu, Asp in the protein and ligands), so the total
charge will be 0.

Thanks in advance,


Rubén Martínez-Buey. PhD student
Protein Function and Structure Dept. Lab. 352
Centro de Investigaciones Biológicas (CIB-CSIC)
C/ Velázquez, 144,  28006  MADRID (SPAIN)
Tlf: +34-91-561 18 00 ext. 4380
Fax: +34-91-562 75 18

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20040427/f499b358/attachment.html>

More information about the gromacs.org_gmx-users mailing list