Dear David,
This is incorrect: the GDP files at the website above should have everything
> you need.
>
There is an .frcmod file there - could you or anyone else outline briefly
how to use just the parameter file to create a unit to load to create a
library file such that minimisation can occur?
(so that other larger complexes with GDP as a substituent can be recognised
when their residue name is 'GDP')
Thanks also to Francois for the resources provided.
Best,
Brandon
On Mon, Jun 18, 2012 at 5:27 PM, David A. Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Jun 18, 2012, Brandon Sim wrote:
> >
> > I am trying to model GDP using AMBER,
> > Total number of electrons: 227; net charge: -2
>
> The total charge of GDP in the deprotonated from you specify appears to be
> -3,
> not -2.
>
> > I am trying to model GDP using AMBER, but I am having trouble using
> > antechamber. I am familiar with the GDP/GTP parameters located at
> > http://www.pharmacy.manchester.ac.uk/bryce/amber#box, but I am assuming
> > (though I may be incorrect) that I still have to run antechamber on my
> GDP
>
> This is incorrect: the GDP files at the website above should have
> everything
> you need.
>
> ....dac
>
>
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Received on Mon Jun 18 2012 - 16:00:04 PDT
