On Wed, May 07, 2014, Mari Mak wrote:
>
> I have built pdb files for boxes of octanol molecules using other programs,
> but I was unable to get Amber to read these files properly.
You probably need to edit those PDB files so that the atom and residue names
exactly match the ones in your Amber library. Without any details, people
on the list won't be able to help very much.
"Packmol" is the program I use for this sort of problem.
> Can Xleap, or
> any of the other utilities within Amber, be used to build a pdb file
> corresponding to a box of several (e.g., a few hundred) octanol molecules?
You can use the "solvateBox" command to do this, and I think it should work
ok for a single solvent molecule. But I'm betting that you would be more
productive in trying to solve your original problem (getting Amber to read pdb
files that were created by other programs).
...dac
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Received on Wed May 07 2014 - 05:30:03 PDT
