AMBER: Unknown atomtypes in amber

From: Nitin Bhardwaj <>
Date: Thu, 27 Oct 2005 12:26:49 -0500

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

How do I rectify the problem? I can manuallly look up the atomtypes
and edit it myself but then do I run the process all over again?
Also I suppose the charge distribution is determined based on the
atomtypes. Does this mean that all the charge distribution does not
hold? Also are my prmtop and inpcrd still valid?

Any help would be greatly appreciated.
Thanks a lot in advance.
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Received on Thu Oct 27 2005 - 18:53:01 PDT
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