[gmx-users] topology

[Justin Lemkul]

On 2/27/17 12:49 AM, RAHUL SURESH wrote:
> I am explaining my issues regarding complex simulation.
>
> I have 200ns conformer(OPLS FF)
>
> I have generated my ligand gro and itp file.(Using topolgen1_1)
>
> I have edited my protein gro file and made it into complex file as per the
> tutorials.
>
> I have made changes to my topol.top file.
>
> Now in my command for em.mdp I am getting 19 errors stating "NO DEFAULT
> BOND TYPE, ANGLE TYPE, ETC."
>
> Can you guide me with this?
>

This means the atom type assignment makes reference to bonded parameters that 
don't exist.  That means one of two things: (1) either the atom type assignment 
is incorrect, requiring manual correction (as the script warns you, as it makes 
a lot of assumptions and is therefore rather dumb sometimes) or (2) you simply 
have a molecule for which parameters do not exist, requiring manual 
parametrization.  For OPLS-AA, this requires QM calculations to get things like 
equilibrium geometries, vibrational frequencies, and dihedral potential energy 
scans.

-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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