VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu May 24 2018 - 08:33:37 CDT

Hi Kelly, the *adamantane* group is already covered in full by CGENFF with
the residue name "ADAM", and you shouldn't need to rederive its dihedrals.

*Amantadine* (i.e. adamantane with an amine group bound to C1) is a minor
extension of that topology, and the parameters guessed by the CGENFF server
are reasonably accurate.

Giacomo

On Wed, May 23, 2018 at 11:07 PM, Peter Freddolino <petefred_at_umich.edu>
wrote:

> Rather than change the level of theory, which really breaks the whole
> parameterization procedure, you are probably better off in your case to
> instead restrict the range of angles that you're sampling. For highly
> constrained ring systems like the one you're working with, it is probably
> better to restrict your scan to a region around the equilibrium geometry
> that could be reasonably achieved in the context of your molecule (and
> then you'll end up fitting the dihedral potential to this - you should also
> consider carefully what multiplicity for the dihedrals are appropriate in
> your case; if the molecule is constrained such that only one region of
> dihedral space can reasonably be sampled, as would be the case for some
> atoms involved in the amantadine ring system, a multiplicity of 1 may be
> appropriate even if the chemistry would typically suggest 3).
>
> Best,
> Peter
>
>
> On Wed, May 23, 2018 at 2:28 PM, McGuire, Kelly <mcg05004_at_byui.edu> wrote:
>
>> I am on the Scan Torsions step of the FFTK plugin, and my molecule has a
>> carbon cage (amantadine). Some of the dihedral scans struggle
>>
>> to finish. I set the scan to do +/- 180 for all of the dihedrals. I'm
>> wondering what the best procedure for a cage type molecule would be
>>
>> for a torsion scan. Most of them finish with the default MP2/6-31(d),
>> but about 5 of them either end with the internal coordinates error,
>> constraints
>>
>> errors, or just stops without errors. However, if I change to
>> HF/6-31(d), they finish with normal termination. I don't fully understand
>> the difference between HF
>>
>> and MP2 other than MP2 is a hartree-fock approximation but with an
>> electron correlation energy correction. How much would it change my
>> results on this
>>
>> step if I used HF instead of MP2, or is there a better way to get the
>> scan torsion to work for a cage molecule? Thanks!!
>>
>>
>> *Kelly L. McGuire*
>>
>> *PhD Scholar*
>>
>> *Department of Physiology and Developmental Biology*
>>
>> *Brigham Young University*
>>
>> *LSB 3050*
>>
>> *Provo, UT 84602*
>>
>>
>>
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin