[gmx-users] Re: No such moleculetype SOL

Justin Lemkul jalemkul at vt.edu
Sat Sep 21 23:18:45 CEST 2013

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 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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