[gmx-users] RE: Define proper set of topology parameters for new molecule in different FF.
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
>> || |
>> | |
>> 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,
>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.
Again the questions are the same as in the first letter.
Thanks a lot.
I`m looking forward to your reply.
Institute of Solution Chemistry, RAS.
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