AMBER Archive (2005)

Subject: Re: AMBER: Unknown atomtypes in amber

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Sat Oct 29 2005 - 14:24:04 CDT

Yes dac,
  You were right.. I actually figured it out later on myself that I
was not loading leaprc.gaff.. Thanks of responding anyways.
Rgds,
Nitin
On 10/29/05, David A. Case <case_at_scripps.edu> wrote:
> 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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