Hello everyone,
I have a couple of questions regarding the ordering of atoms that LEaP generates for a topology file relative to the ordering of the input structure. I'm trying to create a topology file that preserves the following ordering: heavy atoms followed by hydrogens. I've tuned the input PDB to conform to all the atom naming conventions and there are no complaints from tleap regarding the structure. I can save a topology and inpcrd file, but in doing so, the atom ordering gets defaulted to the ordering in the templates. Is there a way to turn this off? Also, when adding explicit solvent and then ions to neutralize the system, do the ion atoms always come after the solute atoms in the topology file regardless if one adds the explicit solvent first then counter ions in tleap?
Thank you for your help!
Cheers,
Andrew
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Received on Mon Aug 15 2011 - 12:30:02 PDT
