On Wed, Nov 09, 2011, Senthil Natesan wrote:
> Initially I tried to set up the system as Jan mentioned, preparing
> single pdb file but due to atom/residue numbering, it didn't work
> well. Probably due to too many ligand molecules (not at the same binding
> pocket) ?
Please post the exact error messages you got from the loadPdb step.
We should emphasize to new users the most common approach: you do indeed
create a single pdb file with all the protein/lipid/ligand/etc groups,
then use solvateOct on that. And, you need to keep editing the pdb file
until LEaP stops complaining. I understand that the error and warning
messages may be hard to understand, which is why I am asking to see them.
>
> p = loadpdb protein.pdb
> l = loadpdb ligand.pdb
> c = combine {p l}
> [addions, solvateoct, saveamberparams]
I agree that this ought to work as well, although it is far less common as an
approach. Are the coordinates of p and l in the output incprd file the same
ones as in protein.pdb and ligand.pdb? If so, this indeed sounds like a bug;
if you can post a (small) example showing the problem, we can take a look at
it.
...thanks...dac
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Received on Wed Nov 09 2011 - 07:30:06 PST
