On Aug 4, 2011, at 6:42 PM, David Cantu <cantudav.amber.gmail.com>
>
> We solvated a system on Xleap that requires many waters. The pdb, prmtop,
> and inpcrd files, after residue number 9,999, started numbering the residues
> with 1.
This seems odd, since neither the prmtop or inpcrd files have any residue numbers at all. It sounds like you may be misinterpreting data in these files.
How did you construct the pdb file? The ambpdb program is probably the best way.
>
> Does this cause a problem in our simulations? We think that when using
> residue number to place constraints it does. We also are not compfortable
> with the idea of two atoms having the same number.
Residues in amber start from 1 and keep increasing. Same for atom numbers. Since pdb files don't have room for incredibly large nmbers of atoms, they may appear odd, depending on how they were made.
...hope this helps....dac
>
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Received on Thu Aug 04 2011 - 19:00:03 PDT
