AMBER Archive (2009)

Subject: Re: [AMBER] reg. GBA

From: case (case_at_biomaps.rutgers.edu)
Date: Thu Nov 12 2009 - 07:02:43 CST

On Thu, Nov 12, 2009, balaji nagarajan wrote:
>
> I have followed the tutorial given for Oxytocin peptide.

Can you give an exact pointer to this tutorial? It sounds old(?), and may
need to be updated.

>
> I have minimized the structure and when I tried to do the
> equillibration i had the problem saying error message "Bad atom type Ip"

This is rather weird, to have such a difference between minimization and MD.
"IP" is an old name for a solvated sodium ion.

> or it is not advaisable to add Sodium for neutralizing the DNA

Generally, there is no need to neutralize DNA when running GB simulations.
Almost all published simulations do not have explicit counterions. A few
groups are exploring adding counterions to GB, but that is an advanced
research topic, requiring lots of thought and testing.

...dac

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