On 6/26/15 7:19 PM, James Lord wrote:
Hi Justin,
I have asked this before, but this time I started up from scratch and used
the input files that I know they are fine but again I am getting this
error, Would you please tell me what is wrong in my topology files and
where about in .top files the bond length are defined?
https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing
There's nothing I can do with a topology that's a series of #include statements.
Please also remind me what this is all about so I don't have to go digging
through the archives for something from a month ago. Lots of things have
happened since then :)
-Justin
Cheers
James
On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 5/16/15 11:35 PM, James Lord wrote:
Hi Justin
Thanks for this. Can you tell me which step(s) this bond length is
defined????
What should I do (redo) to resolve this issue?
The bonds are defined in the topology. The DD algorithm reads what's in
the coordinate file and builds cells based on the geometry it finds there.
Without a full description of what's in your system, what steps you've
taken to prepare it (full commands, in order), there's little I can suggest
because it would all be guesswork.
-Justin
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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