On 9/22/13 10:10 PM, Jonathan Saboury wrote:
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.
Hm...not sure what the matter is. Added a forcefield as well as spc.itp to
the .top file made by acpype. Still getting the error "Fatal error: No such
moleculetype SOL"
Here is a list of commands and explanations of what I did:
http://pastebin.com/raw.php?i=V5wrRdme
Here is the .top: http://pastebin.com/raw.php?i=LzCANQZw
Here are the files I am using: http://www.sendspace.com/file/5ps0i1
I should have seen this before. The default spc.itp is not compatible with
AMBER. Have a look at the actual contents of spc.itp:
; This file is for backward compatibility only.
; Please directly include the spc.itp file from your force field directory.
#ifdef _FF_GROMACS
#include "gmx.ff/spc.itp"
#endif
#ifdef _FF_GROMOS96
#include "gromos43a1.ff/spc.itp"
#endif
#ifdef _FF_OPLS
#include "oplsaa.ff/spc.itp"
#endif
That said, there is an spc.itp within the AMBER subdirectories that needs to be
#included more explicitly, i.e. #include "amber99sb.ff/spc.itp"
May I ask why you are using SPC? The AMBER force fields were parametrized with
TIP3P, so I see no viable reason to use a different water model.
It is important to note that genbox did not add the amount of cyclohexanes
added to system in the .top (it did do it for the waters though). Perhaps
that is a bug?
It's not a bug, because genbox does not advertise such a feature. genbox is
hard-coded to only ever deal with water. Anything else is up to the user.
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 see, interesting. Added it to the .top :)
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 ;)
As you know I am using acpype, is it any better? What do you use?
Any force field can be parametrized to give correct target data, especially for
a molecule as simple as cyclohexane. What I use is a complex question, because
it depends entirely upon the task at hand :)
-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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