On Mon, Nov 07, 2005, Whitney Allen wrote:
>
> I was trying to use the Case and Meyer's lib and frcmod files for the
> modified bases of tRNA-Phe which I found on the Amber Parameters Database
> (http://pharmacy.man.ac.uk/amber/). I tried loading them into the Amber 8
> xleap module with the 6tna.pdb structure to see if I could get out prmtop
> and inpcrd files. Unfortunately I got some unrecognized atoms and a few
> fatal errors. Here are the commands and errors. Note that I saved the FRCMOD
> file as tRNA.frcmod and the OFF file as tRNA.lib.
>
>
> Unknown residue: MO4 number: 77 type: Nonterminal
> Unknown residue: MO6 number: 78 type: Nonterminal
> Unknown residue: MO5 number: 79 type: Nonterminal
>
Note that the tRNA itself ends at residue 76. What you are trying to read in
are hydrated magnesium ion sites. You will either have to strip these from
the PDB file, or define some residue types that accommodate them. Handling
divalent ions with molecular mechanics force fields is still a difficult
problem. You might check the literature to see what others have done when
simulation tRNA.
....good luck...dac
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Received on Mon Nov 07 2005 - 16:53:00 PST
