AMBER Archive (2005)

Subject: Re: AMBER: Unknown atomtypes in amber

From: David A. Case (case_at_scripps.edu)
Date: Sat Oct 29 2005 - 12:06:20 CDT

On Thu, Oct 27, 2005, Nitin Bhardwaj wrote:

> I modelled a non-standard lipid molecule. I ran antechmaber
> and crated the *.prepin file. I then checked the molecule using
> "check" command. There was no warning or missing parameters. When I
> load it in xleap and ask it to Display the types,

How did you "load it in xleap"? Did you remember to source the leaprc.gaff
before-hand? If you can't figure this out, please send the exact commands you
used in LEaP.

> some of the Hydrogen
> atoms are labelled as 'hx' and a nitrogen as 'n4 ' and a phosphorus as
> 'p5'. I looked up the table of atomtypes for both GAFF and AMBER
> atomtypes. They are not there.

I am confused here. Which "table of atomtypes" are you referring to? These
atom types are certainly in gaff.dat.

> In the 'Edit Selected atoms' table, there is a question mark against the
> atomtype these non-standard atoms.

This sounds like you didn't source the appropriate leaprc file.

...good luck....dac

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