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

[Hassan Aaryapour]

use swissparam server, http://swissparam.ch/

On Mon, Jul 27, 2015 at 3:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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 molecule.
>
> -Justin
>
> --
> ==================================================
>
> 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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