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

Andrey Frolov andr.frolov at rambler.ru
Tue Aug 5 18:48:04 CEST 2008

>>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
>>         ||             |
>>          C-------O1----C2----Hc4
>>          |             |
>>    Hc3-- C1--Hc2       Hc6
>>          |
>>          Hc1
>>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,

> >>MMFF94.
 >> 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,

>You should describe the values of those parameters you want either
>constrain or simulate with intramolecular parameters. Evidently, you
>need a set of values completely determining the geometry of your
>molecule. However, you make want some atom groups to rotate during the
>simulation, then you need not to give the respective numbers.

>For an example just see the existing FF provided with GROMACS..

Dear Dr. Chaban,

Thanks a lot for your reply.
I`m very sorry but it seems that you did not properly 
understand the goal of the letter.

1) The aim is to create a topology in certain FF
that`s why we should follow the methodology of parametrization of this FF (to my mind).
 |=> the "topology graph" (gmx topology  without  all FF values) is not FF independent.
	Am i right?
2) To describe exact 3D structure of molecule we should 
    define 2*N-5 angles (bond angles or/and dihedrals) (N-number of atoms),
    besides of all bonds.
     (that`s my empirical formula).
    In gmx provided topologies there is no possibility to understand
    what is the final topology of residue (RTP file: there are only bonds
        and improper dihedrals, what about others: bond angles, and proper dihedral?)
    share/top/urea.itp: there are all possible bond angles
  H            8 proper dihedrals (max value)
  |            3 improper dihedral (max value) 
The set of parameters is more then enough.

    share/top/benzamide.itp: (that is not realy benzamide if we`ll see WIKIpedia)
     H            there are set of parameters that is greater that it
     |             should be to define 3D structure, but less then the max value.
 __  |
/O \_C--N--H
\__/    |

Again the questions are the same as in the first letter.

Thanks a lot.
I`m looking forward to your reply.
Andrey Frolov.

Institute of Solution Chemistry, RAS.
Ivanovo, Russia.


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