[gmx-users] #include section in a .top file

[Justin Lemkul]

On 5/26/15 8:57 AM, soumadwip ghosh wrote:
> Plaese ignore the previous mail.
>
> Thanks Justin for your help as always. Actually, the atomtype CR was
> common to both the building units of the polymer as well as the cation
> built by SWISSPARAM. I generally dont use maxwarn at all but I too
> thought of the warning being not harmful  since the grompp was
> complaining due to the atomtypes were same in two of the .itp files. I
> would like to ask whether the construction of my .top file is right or
> not. If in general, I have made two or more ligands from some other
> source compatible with my force field , is the way I have mentioned
> two atotypes.itp immediately after ff description is correct or not so
> that I dont have to deal with this issue in future.

Yes, it's fine.

> Also, in the given context is it really possible to do something so
> that gromacs does not show this 'overriding atomtypes' error? For once
> I thought it would land me in different problems ( -maxwarn 1 option)
> while running solvent relaxation and equilibration.
>

Like I said, and you've recognized above, you're not overriding anything.  It's 
just redundant.  If you don't want to see the warning, get rid of the 
redundancy.  If different molecules share parameters, they only need to be 
declared once.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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