Dear Gmx users,<div><br></div><div>I had been using Gromacs for couple of years and always found these forums quite helpful. Right now again I have another question to ask that I was not able to figure out yet myself and reading previous posts.</div>
<div><br></div><div>I need to the ffG53a6 forcefield to be able to recognize the non-standard amino acid like AZE (Azetidine-2-carboxylic acid) which closely resembles Proline, but lacks CH2 group in the ring of the side-group, making the R-group a 4 member ring instead of 5. Thus, this amino acid has very close chemical structure to the Proline which is properly defined in the *.rtp file as below</div>
<div><br></div><div><div>[ PRO ]</div><div> [ atoms ]</div><div> N N 0.00000 0</div><div> CA CH1 0.00000 1</div><div> CB CH2R 0.00000 1</div><div> CG CH2R 0.00000 2</div><div>
CD CH2R 0.00000 2</div><div> C C 0.450 3</div><div> O O -0.450 3</div><div> [ bonds ]</div><div> N CA gb_21 </div><div> N CD gb_21 </div><div> CA CB gb_27 </div>
<div> CA C gb_27 </div><div> CB CG gb_27 </div><div> CG CD gb_27 </div><div> C O gb_5 </div><div> C +N gb_10 </div><div> [ angles ]</div><div>; ai aj ak gromos type</div>
<div> -C N CA ga_31 </div><div> -C N CD ga_31 </div><div> CA N CD ga_21 </div><div> N CA CB ga_13 </div><div> N CA C ga_13 </div><div> CB CA C ga_13 </div>
<div> CA CB CG ga_13 </div><div> CB CG CD ga_13 </div><div> N CD CG ga_13 </div><div> CA C O ga_30 </div><div> CA C +N ga_19 </div><div> O C +N ga_33 </div>
<div> [ impropers ]</div><div>; ai aj ak al gromos type</div><div> N -C CA CD gi_1 </div><div> CA N C CB gi_2 </div><div> C CA +N O gi_1 </div><div> [ dihedrals ]</div>
<div>; ai aj ak al gromos type</div><div> -CA -C N CA gd_14 </div><div> -C N CA C gd_39 </div><div> CA N CD CG gd_39 </div><div> N CA CB CG gd_34 </div>
<div> N CA C +N gd_40 </div><div> CA CB CG CD gd_34 </div><div> CB CG CD N gd_34 </div></div><div><br></div><div><br></div><div>The question is how can I derive from this Proline definition topology the corresponding topology for AZE? The problem is that I do know how to interpret the each column such as the "gromos definition" column gd_14, etc, as well as other columns..... Where can I get information or tutorials about this important issue on how to create own topology files? Maybe someone can explain those columns in easy terms? What are corresponding atoms referred by atom names in the final structure as the there is not ASCI diagram of those as I've seen in AMBER tutorials? </div>
<div><br></div><div>Also I am interested in knowing on how the topology files are created from scratch?</div><div><br></div><div>Any help will be greatly appreciated. </div><div><br></div><div><br></div><div>Kirill</div><div>
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