AMBER Archive (2006)

Subject: Re: AMBER: problem loading forcefield leaprc.ff86

From: David A. Case (case_at_scripps.edu)
Date: Fri May 19 2006 - 10:45:33 CDT

On Fri, May 19, 2006, Mahalakshmi Sahasranaman wrote:
>
> I am using amber8 and I am trying to load my dna using leaprc.ff86. I have
> introduced a TER card
> between residue 10 and residue 11 as indicated in the amber tutorial.
> When I load leaprc.ff86 using xleap for vacuum simulations, it says
> > adna1 = loadpdb "a-dna.pdb"
> Loading PDB file: ./a-dna.pdb
> Unknown residue : C5 number :0 type : Terminal/beginning

The 86 (aka "91") force field uses a different nomenclature for nucleic acids,
where the phosphate groups are in separate residues. If you really want to
carry out this caclulation, you will need to study the library files, and
convert the atom and residue names in your pdb file to match those in the
library. Basically, Amber doesn't really offer much support any more for
the 1986 force field, nor do we encourage people to use it.

...good luck....dac

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