[gmx-users] Changed order of molecules in top

Justin Lemkul jalemkul at vt.edu
Wed Jul 2 17:29:25 CEST 2014

On 7/2/14, 11:17 AM, Emma A wrote:
>> Without seeing the full contents of all the files, none of this really makes
>> sense.  If you can provide a link to download the full (1) topology and all
>> related .itp files, (2) coordinates, and (3) .mdp files, I will take a look.
>> -Justin
> Hi again,
> thanks a lot for taking your time.
> Here is a link to the top (and test.top with just one IMI), the gro, the
> itp´s, and the mdp files.
> https://www.dropbox.com/s/dmz41drsjr0bqkn/ZnHis2Wa2.tar.gz
> I hope this kind of link works.
> Best regards,
> Emma

Here's your problem:

[ molecules ]
; Compound        #mols
IMI             1

is in imiamberrtp.itp and it should not be.  An .itp file specifies a 
[moleculetype] and associated parameters.  The [system] and [molecules] 
directives are system-level instructions.  So what's happening is you're telling 
grompp that there is an IMI molecule as soon as you #include the .itp file.  A 
bit surprising that there aren't any other fatal errors, because technically 
this breaks the topology order.  Remove [system] and [molecules] from this .itp 
file, correct the [molecules] directive to specify 2 IMI in the .top, and you 
should be fine.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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