[gmx-users] Topology file for serotonin (5-HT)

Justin Lemkul jalemkul at vt.edu
Mon Jul 27 13:43:44 CEST 2015

On 7/27/15 1:03 AM, Ganesh Shahane wrote:
> Hi Justin,
> Yes. I tried the same, but during the preparation of the .tpr file using
> grompp it gives an error saying "No default proper dihedral types" for 3
> dihedral angles which are not present in the ffbonded.itp of the charmm36
> force-field. These 3 dihedrals consist of atoms that encompass the alkyl
> amine and the indole groups of serotonin.
> Now, if I remove these dihedrals in question from the serotonin's .itp file
> which I have prepared, the simulation runs just fine. I am trying to
> calculate the free energy of solvation for serotonin. Considering this, is
> it okay to ignore some of these dihedrals?

Absolutely not.  You can't just delete inconvenient interactions.  If there are 
missing parameters, you need to derive suitable dihedral terms.  Or just throw 
the molecule at ParamChem and see how it does.  CGenFF should work fine for this 



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


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