[gmx-users] Define proper set of topology parameters for new molecule in different FF.

Andrey Frolov andr.frolov at rambler.ru
Tue Aug 5 10:09:22 CEST 2008

Dear gmx-users,

I want to construct TOPOLOGY of many different molecules using different 
Force Fields (FF).

If i want to describe , for example, METHYL ACETATE in OPLS-AA force field

            O               Hc5
            ||                |
            |                 |
 Hc3-- C1--Hc2       Hc6
1) I'll find all ATOM TYPES in oplsaa, let`s imagine that they are like 
in the image above.
2) then i describe all BONDS and PAIRS
3) then i should define BOND ANGLES
      but how much angles should i describe?
      PRODRG and topologies in share/top give all possible angles,
      but is there overestimation of FF energy in such cases, as:
            angle O-C-C1
            angle O-C-O1
            angle O1-C-C1
        3 adjoining angles in planar group?
4) then i should define PROPER and IMPROPER DIHEDRALS.
      Should i define all possible DIHEDRALS as it is made in GMX 
      Or should i define only those DIHEDRALS that are exist in chosen FF?
          Are there any rules how to chose these parameters?

For the first view it seems that you should chose these parameters like 
they were parametrized in chosen FF.
=> the "topology graph" (gmx topology  without  all FF values) is 
different for different FF?
      Am i right?
      And in order to describe the molecular TOPOLOGY in CERTAIN FF we 
should know the special "rules" for THIS FF,
=> mail to author of FF or read initial papers.
      Am i right?

The initial papers do not contain CLEAR description of how to chose 
proper set of parameters.
   I`m interested in GROMOS, OPLS-UA, OPLS-AA, AMBER-UA, AMBER-AA FF, 
   So, if you know any rules or useful links i'll be very thankful.
I`m very sorry if my questions are mentioned already, but i did not find 
the answer in mailing-list.
Kindest regards,


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