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

[Ganesh Shahane]

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?

Thanks!

On Mon, Jul 27, 2015 at 5:43 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/23/15 2:10 AM, Ganesh Shahane wrote:
>
>> Dear Gromacs Users,
>>
>> I am looking forward to performing some simulations of a receptor bound to
>> serotonin (also known as 5-HT). Does anybody have the .itp file of
>> serotonin for the charmm27 or charmm36 force field? Thank you!
>>
>>
> It's very straightforward to combine existing parameters to make this
> simple molecule (indole + hydroxyl + alkyl amine).  CHARMM covers all of
> these functional groups easily.
>
> -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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-- 
Best Regards,
Ganesh Shahane