[gmx-users] RE[4]: Define proper set of topology parameters for new molecule in different FF.

[Vitaly Chaban]

>>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
>>share/top/urea.itp?
>>     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)
> N--H
> |
>O=C--N--H
>    |
>    H
>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.
>    N--H
> __  |
>/O \_C--N--H
>\__/    |
>       H
>
>Again the questions are the same as in the first letter.
>
>Thanks a lot.
>I`m looking forward to your reply.
>Andrey Frolov.

If you have found all the atom types you need in the OPLSAA try to use
'x2top' in order to generate a topology for a certain compound from
your PDB(or xyz?) structure.
It seems to be the quickest way for your persue.


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban