AMBER Archive (2005)

Subject: Re: AMBER: loading pdb

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed May 18 2005 - 15:21:24 CDT

Hi,

If you just started using on AMBER, I would strongly advise you to follow
the tutorials, especially the workshop tutorial. I am working on RNA
structures, and therefore did not have any experience with aminoacids, but
I guess your problem lies in the residue names. In the RNA case, there is
not just 1 residue defined for a nucleic acid. Let's say we want to have a
cytosine molecule in the strand. Depending where in the strand it is, you
should use either RC, RC3, RC5. If it is in the middle of helix (meaning
connected from both ends), u should use RC. If its at the 3' end, u should
use RC3, and if its at the 5' end, u should use RC5. If you want to
understand these different residues, go to

$AMBERHOME/dat/leap/lib

directory, and analyze the library your force field is using. Or, while u
are in xleap and loaded the force field parameters, use the command 'list'
to see all residues defined in that force field. And by using the command
'edit <RESIDUE NAME>' u can visualize that particular residue. If u are a
newcomer, it is best to, therefore, follow the tutorials to get familiar
with the program. AMBER just follows the commands/rules. If you do not
have a residue defined in your force field (or modified force field file),
xleap will not understand that particular residue defined in the .pdb
file. I hope this might help.

Best,

On Wed, 18 May 2005 cbala_at_igib.res.in wrote:

>
> I am a research student from India. I have just now started using AMBER8.
> i have to load a pdb file in Leap.I have already edited pdb file and
> deleted all unwanted stuff like hetero atom etc in the file.
>
> while loading the pdb file in Leap, i get a message like "UNKNOWN
> RESIDUE.... TYPE:Non terminal" for some amino acid residues.
>
> Kindly suggest me what i have to do to rectify this error.
>
> Thanks,
> C.BALASUBRAMANIAN,
> IGIB,
> DELHI, INDIA.
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
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