AMBER Archive (2005)

Subject: Re: AMBER: nucgen problem

From: David A. Case (case_at_scripps.edu)
Date: Tue Jun 07 2005 - 15:17:12 CDT

On Tue, Jun 07, 2005, cbala_at_igib.res.in wrote:
>
> 2)Sir reg. my second question i have attached the pdb file here (GCAT). i
> could understand that the numbering given by insightII is the problem
> when it is read in xleap.can anyone help me in solving it.i used
> leaprc.ff99.

Your input pdb file has a phosphate group at the 5' terminus of both strands.
If this is what you really want, you will have to remove the PdbResMap
commands from the leaprc file, since those assume you have a
non-phosphorylated 5' residue (as in most oligonucleotides.) If you don't
want the dangling phosphate, you will have to remove those atoms manually from
the PDB file.

...dac

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