> On Apr 16, 2017, at 11:17 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> Unfortunately, I have been (and for the coming week will be) extremely
> busy so my response time is going to be down.
>
> However, I did manage to look at your files and figure out the issue.
> Your original topology is making use of a 4-point water model. By
> default cpptraj does not print out extra points into PDB files. I
> forget the original rationale for this but I'm pretty sure there was a
> good reason.
Most modeling workflows would likely struggle with waters that had more than 3 atoms (LEaP included, probably). And since PDB files are generally bad as a coordinate file format, I think the current default is best. I vaguely recall the conversation about that behavior, and I think that was the general consensus.
All the best,
Jason
--
Jason M. Swails
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Received on Sun Apr 16 2017 - 20:00:02 PDT
