AMBER Archive (2009)

Subject: Re: [AMBER] Modification of His

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon May 18 2009 - 07:31:33 CDT

On Mon, May 18, 2009, Jorgen Simonsen wrote:
>
> I think tihe problem is that I need to find a new pdb name for my nitrogen
> atom instead of ND1 which is the same as in histidine.

I don't think so. As long as the residue name is different, ND1 of HIE will
not get mixed up with ND1 of your residue.

In the leaprc file it is defined as
> { "N*" "N" "sp2" }

Try adding this:

     { "YA" "N" "sp2" }

That says that atom type (*not* atom name) YA is a type of nitrogen that has
an sp2 parameterization.

>
> so I cannot use "N*" "YA" "sp2". I have performed a small md simulation of
> my residue and the ring is not planar - could that be due to it not being
> sp2-hybridized?

I don't think so(?), but do the test. Do you have the same torsion terms for
atom type YA as for atom type N*?

...dac

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