How about your suggested warning message including a suggestion to do 'strip
.EPW'?
Jim
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Monday, April 17, 2017 8:40 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] cpptraj creates pdb file it cannot read
I think the best solution here will be to have CPPTRAJ print a warning that
extra points will be excluded from PDB files when 'include_ep' is not
specified.
-Dan
On Sun, Apr 16, 2017 at 10:56 PM, Jason Swails <jason.swails.gmail.com>
wrote:
>
>> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Apr 17 2017 - 13:30:03 PDT
