[gmx-users] itp file using Gromos96 parameters

[Alan Wilter Sousa da Silva]

Hi Anton,

	Thanks a lot!
	However I have a few more doubts.

	In file ffG43a1bon.itp we have for Gromos bond-angle parameters:

#define ga_1         90.00      420.00
; NR(heme)  -  FE  -  NR(heme)  100
;
etc...

	As I believe, grompp will read #define ga_? line with its
parameters (for ga_1: angle = 90.00 and constant = 420.00).
	My Gromos96 parameters for constant are in other unit system (I
think) and correspond to the last value in the commented line, for ga_1:
; NR(heme)  -  FE  -  NR(heme)  100
so constant = 100.

	 What is constant according to this table?  How can I achieve
these values, since I cannot see a correspondence?

Many thanks in advance.

On Wed, 5 Jun 2002, Anton Feenstra wrote:

> Alan Wilter Sousa da Silva wrote:
> >
> > I can figure out that if I include new ga_?? parameters in the
> > ffG43a1bon.itp file I could get to complete my itp drug file.
>
> Correct.
>
> > Nevertheless, would GMX understand if I explicit the parameters in the
> > drug itp file, like that?
> >
> > [ angles ]
> > ;    ai     aj     ak  funct  ang.  const.
> >       1      5      4     2  110.0   100.0
> >       2      6      7     2  ga_12 ;  C -  CH2 -   OA   110.0  109.5
> >       6      7      8     2  ga_11 ;CH2 -   OA -    C    95.0  109.5
> >       7      8      9     2  112.0   120.0
> >
> > or I'd have change funct from 2 to 1 and so to explicit my parameters.
> > Would GMX still respect Gromos96 force field?
>
> Yes, GMX (grompp in this case) will not see a difference between the
> ga_?? defines and explicit parameters. You can choose wheter to use
> angle type 1 or 2, but 2 would be consistent with the Gromos96 (43a1)
> forcefield. Gromacs will still use all the parameters as defined in
> the Gromos96 forcefield for all interactions that you don't change
> explicitly.


-- 
-----------------------
Alan Wilter S. da Silva
-----------------------
 Laboratório de Física Biológica
  Instituto de Biofísica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil