[gmx-users] D-aminoacids

Anton Feenstra feenstra at few.vu.nl
Mon Oct 4 18:00:18 CEST 2004

Hi Andreas,

I'll start with an *IMPORTANT* *REMARK*!

The *OLD* Gromacs forcefields (ffgmx and ffgmx2) are severely *DEPRECATED*.
Unless there are very compelling reasons, you *SHOULD* *NOT* (*EVER*!) *USE* *THEM*!

The *NEW* Gromos forcefields (ffG43*) are *MUCH* *BETTER*.
The *NEW* OPLS forcefield (ffOPLS) is *MUCH* *BETTER* and *ALL* *ATOM*.

Having said that, hopefully for everyone to understand, please find my comments
to your question(s) below.

Andreas Kukol wrote:

> Dear all,
> If I want to use a D-amino acid residue as opposed to the natural L-aminoacid is it correct to modify the improper dihedral in the .top file created by pdb2gmx, by specifiying the improper dihedral as -35.364 degrees:
> [ dihedrals ]
> ;  ai    aj    ak    al funct            c0            c1            c2            c3
>     4     1    20     6     2          -35.364  (<-- I added this number only)
> (  CA   N     C    CB   <-- atom names for clarification)

Yes and no. Yes, it is correct to specify -35 something degrees, but not as you
did it in the example. Problem is here that the other parameters (e.g., force
constant) will not be added, and you will end up using a 'zero' force.

Two ways to fix this:
1) specify the other parameter(s), in addition to the angle, explicitly; or
2) change the order of the middle two atoms (i.e., CA C N CB) with the normal
    +35 degrees.

> Is it correct that when using the GROMACS all hydrogen forcefield, I don't need to change anything, as long as the starting structure has the correct stereochemistry ?
> Intersting is, that even with the 'all hydrogen' forcefield the impoper dihedral shown above is generated.
> I would be grateful for any confirmation/clarification.

*FIRST* read my comments at the top of this mail!

The gromacs all H forcefield (ffgmx2) is *identical* to the 'normal' gromacs,
except for the explicit inclusion of all H-atoms. The additional H's do not\
have charges, and do not have any VdW interactions. So, in effect they are
only masses, connected by bonds & angles to the rest of the molecule, and
except for changes in the degrees of freedom they do not add anything to the
physics of your system. For sake of simplicity, during creation of the ffgmx2
forcefield, all other parmeters and interactions were kept identical.


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |

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