>>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: [EMAIL PROTECTED] skype: vvchaban _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
