Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help

From: David A. Case <case.biomaps.rutgers.edu>
Date: Sat, 19 Nov 2011 00:13:26 -0500

On Fri, Nov 18, 2011, Crystal.CHIA-YU Ku wrote:

> ...even though until know all information in hand point that
> in pH 7.0, thiamine monophosphate has +1 net charge and two hydrogen
> on the phosphate group...

I was arguing based on chemical intuition.

If you have "known information" that thiamine monophosphate has a +1 charge
at pH 7, you can use that information. But I'd still suggest double-checking
your sources.

Francois has provided excellent advice on the best way to work with
thiamine monophosphate, and I'd recommend doing what he suggests.

...regards...dac


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Received on Fri Nov 18 2011 - 21:30:04 PST
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