[gmx-developers] calculating gbsa parameters for metal ion

Erik Lindahl erik.lindahl at gmail.com
Fri Mar 31 19:11:53 CEST 2017

Hi Javaria,

As you have probably seen from a number of mails, this list is intended for
Gromacs developers to help each other in developing the code. Please move
all usage questions to gmx-users.

The general answer for how to find new parameters is that you'll first have
to read the papers for the force field and algorithm to understand it (e.g.
HCT Generalized Born) and then either find parameters in the literature of
learn how to derive them.



On Fri, Mar 31, 2017 at 8:09 AM, Javaria ashraf <jia_ashraf at yahoo.com>

> Hello and greetings
> i am simulating my protein in implicit solvent. the protein has ca2+ ion
> in it. the gbsa.itp file doesn't have parameters for any ion.
> how can i add parameters of my ion?
> As mentioned in tutorial.....
> [ implicit_genborn_params ]
> ;Atomtype sar st pi gbr hct
> Values in columns 1-3 are not currently used. Column 4 contains the atomic
> van der Waals radii, which are used in computing the Born radii.
> the van der Waals radii of ca2+ is 0.231? is it right? or how can i
> calculate the hct?
> thank you
> --
> Gromacs Developers mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-developers_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
> or send a mail to gmx-developers-request at gromacs.org.

Erik Lindahl <erik.lindahl at gmail.com>
Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm
Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20170331/0c023401/attachment.html>

More information about the gromacs.org_gmx-developers mailing list