[gmx-users] Re: No such moleculetype SOL
jalemkul at vt.edu
Mon Sep 23 04:18:09 CEST 2013
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
>> 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:
> 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.
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
>> 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
>> example for doing a tutorial rather than trying to teach people how to use
>> 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 A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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