AMBER Archive (2006)

Subject: Re: AMBER: LEAP - "could not find type: NH"

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Sep 08 2006 - 17:42:46 CDT

Dear Seth,

There are missing force field parameters for your case. I guess u have
atom types named HN and NH. You need to define these types in a modified
force field file (aka .frcmod file). Also, u need to define the missing
bond lenth/angle/dihedral parameters in the .frcmod file. For more
information about .frcmod file, u can go to the following address:

http://amber.scripps.edu/formats.html#frcmod

For some example files, go to your "$AMBERHOME/dat/leap/parm" directory.
You will see some files like frcmod.*. You can check them out to
understand the format of .frcmod files. Hope this helps.

Best,

On Fri, 8 Sep 2006 sethl_at_gatech.edu wrote:

> Dear Amber Community,
>
> When doing a "saveamberparm" I get the following:
>
> Building topology.
> Building atom parameters.
> For atom: .R<UNK 25>.A<H 2> Could not find type: HN
> For atom: .R<UNK 25>.A<N1 7> Could not find type: NH
> For atom: .R<UNK 25>.A<H8 8> Could not find type: HN
> For atom: .R<UNK 25>.A<H9 9> Could not find type: HN
>
>
> and the UNK residue is one that was created using antechamber. I'm loading in
> the leaprc.rna.ff99 and the leaprc.gaff force fields. What am I doing wrong?
>
> Thanks,
> SETH
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
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  - http://www.pas.rochester.edu/~yildirim/			-
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