On 9/21/13 5:15 PM, Jonathan Saboury wrote:
Have a look at how Justin's tutorial's .top gets access to a water
topology.
Mark
Thank you very much for the response Mark!
I've looked at his .top and it seems to me that how he included it is by
adding "#include spc.itp". I've added that line to cyclohexane.top before
and after the "#include "cyclohexane.itp" with no success (same error as
before).
Then something is wrong with the way you've done it, because the job of spc.itp
is to define the [moleculetype] SOL and all its relevant parameters.
I also saw that he added a force field. Would I need to do this if I am not
interested in a protein?
You need a parent force field that defines all the bonded and nonbonded
interactions in the system. Whether or not this is one that comes with Gromacs
or one you design yourself, you still have to satisfy all of the internal
mechanics (see Chapter 5). Whether or not there is a protein is completely
irrelevant; force fields do much more than just proteins.
I want to avoid using PRODRG because it is online which admins can easy see
what I uploaded. I feel much more comfortable using programs on my system
(the reason I am using acpype).
Well, PRODRG parameters are pretty low-quality anyway, but it's a convenient
example for doing a tutorial rather than trying to teach people how to use other
external software ;)
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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