Hello Sir,
Thanks for your response. You suggested that the Mg2+ parameter have
problem.
Can I use the latest Mg2+ parameter defined by Villa et.al. JPC (2012) (Ref
: Magnesium Ion water coordination and exchange in biomolecular simulations)
or the old one by Aqvist et.al (1990) ?
As this was suggested in the mailing list (
http://archive.ambermd.org/201205/0488.html).
Regarding the the Mn2+ parameter can I use the Mn2+ parameter defined by
Bryce Group (
http://www.pharmacy.manchester.ac.uk/bryce/amber#ion). There
is Mg2+ parameter also.
What is your suggestion ?
Many Thanks
----indrajit
---------------------------------------------------------------------
Indrajit Deb
Kolkata, India.
Mob: +919239202278
On Mon, Jun 25, 2012 at 5:12 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Sun, Jun 24, 2012, Indrajit Deb wrote:
> >
> >
> > Starting new chain with MG2
> > Starting new chain with MG2
> > Creating new UNIT for residue: MN sequence: 12
> > Starting new chain with
> > Created a new atom named: MN within residue: .R<MN 12>
> > Starting new chain with TP3
> > Starting new chain with TP3
> > Starting new chain with TP3
> > Starting new chain with TP3
> > Starting new chain with TP3
> > Starting new chain with TP3
> >
> > My questions are:
> >
> > 1. Is it working with crystal waters ?
>
> Looks OK to me.
>
> > 2. Is it working with the Mg2+
>
> Yes, but bear in mind that Mg2+ parameters have problems.
>
> > 3. How to get the Mn2+ parameters ?
>
> I don't know. You could think about replacing Mn2+ with Mg2+.
>
> ....dac
>
>
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Received on Tue Jun 26 2012 - 01:00:05 PDT
