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

Vitaly Chaban chaban at univer.kharkov.ua
Wed Aug 6 11:33:51 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)
> 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

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