[gmx-users] No default Ryckaert-Bell. types for proline

[Justin Lemkul]

On 6/2/15 8:51 PM, Kevin C Chan wrote:
> Thanks Justin,
>
> I'm sorry that I'm not clear with what do you mean by "so you can likely
> just use the same parameters in ffbonded.itp for this dihedral in the
> zwitterionic form".
>

The Pro dihedral term for this torsion is the same, irrespective of whether it's 
N- or C-terminal.  From ffbonded.itp:

   C      CT_2   N      CT_3    3     -5.72371 -18.33847  -5.23419  29.29636 
0.00000   0.00000 ; Pro (fit to AM1) CD-N-CA-C, JT-R 2/10/97
   C      CT_2   NT     CT_3    3     -5.72371 -18.33847  -5.23419  29.29636 
0.00000   0.00000 ; Pro (fit to AM1) CD-N-CA-C, JT-R 2/10/97
   C_3    CT_2   N      CT_3    3     -5.72371 -18.33847  -5.23419  29.29636 
0.00000   0.00000 ; Pro COO- terminus.
   C_3    CT_2   NT     CT_3    3     -5.72371 -18.33847  -5.23419  29.29636 
0.00000   0.00000 ; Pro COO- terminus.

All the same, so the parameters for the zwitterionic species can likely be 
copied to your missing interaction.

> Also as I have mentioned before, when I look into the line 161, it refers
> to a dihedral term concerning (CD N CA C) which is not able to be found in
> ffbonded.itp. However, other dihedral terms such as (CD N CA CB) or (CD N
> CA HA) which are also not found in itp do not report such error and I was

Atom names and atom types are entirely different concepts.  grompp doesn't care 
what you call your atoms (atom name), but it does care what chemical 
characteristics they have (atom type).

> successful to grompp after commenting out the line 161. So why would this
> happen?
>

Don't ever comment out lines because of issues like this.  By doing so, you're 
saying that torsion contributes nothing to the energy function, which is wrong. 
  I suggest copying the above parameters to the correct sequence of atom types. 
  Stuff like this happens all the time.  Force fields are massive entities, and 
are added to incrementally as need arises.  A zwitterionic proline is probably 
not something that people commonly use, and its the most complex case due to the 
chemical nature of it.  It's entirely possible that the .tdb entries were simply 
added by analogy to existing groups as a convenience and never fully tested.

-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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