Justin, hello!
I've found that D and L-isomers must be topological identicaly so I've used topology of Leu and Val residues for Dle and Dva resp. I've added information about topology of that two residues to the .rtp .hdb of my force field as well as to the <http://www.gromacs.org/Documentation/File_Formats/.rtp_File> residuetypes.dat<http://www.gromacs.org/Documentation/File_Formats/residuetypes.dat> Then I've succsesfull generated topology for gramicidin via pdb2gmx. I have only questions about two terminal CAP groups used in the Gramicidin It was FOR group on the C-end HETATM 1 C FOR A 1A -3.690 -1.575 -2.801 1.00 0.00 C HETATM 2 O FOR A 1A -3.774 -1.363 -1.586 1.00 0.00 O HETATM 3 H FOR A 1A -4.305 -1.047 -3.545 1.00 0.00 H and the ETA group on the N-end HETATM 267 C1 ETA A 15A 5.148 -0.421 8.762 1.00 0.00 C HETATM 268 C2 ETA A 15A 3.657 -0.080 8.832 1.00 0.00 C HETATM 269 N ETA A 15A 2.813 -1.244 8.933 1.00 0.00 N HETATM 270 O ETA A 15A 5.921 0.752 8.985 1.00 0.00 O HETATM 271 1HN ETA A 15A 2.507 -1.491 9.845 1.00 0.00 H HETATM 272 HO ETA A 15A 5.736 1.339 8.244 1.00 0.00 H HETATM 273 1H1 ETA A 15A 5.410 -1.174 9.531 1.00 0.00 H HETATM 274 2H1 ETA A 15A 5.374 -0.849 7.759 1.00 0.00 H HETATM 275 1H2 ETA A 15A 3.383 0.525 7.938 1.00 0.00 H HETATM 276 2H2 ETA A 15A 3.492 0.565 9.718 1.00 0.00 I could not find good analogue for that groups in Amber force field so I've desided to deleate that groups temporary. Could you tell me how I can add possible Caps on the C and N terms of each chain of my molecule via pdb2gmx ? In one tutorial I've found the -term function for that but in my case system didnt suggest me to add new caps James 2011/10/28 Justin A. Lemkul <jalem...@vt.edu> > > > James Starlight wrote: > >> Dear Gromacs users! >> >> I've forced with some problem of preparing topology of my input pdb via >> pdb2gmx. >> >> My input structure( gramicidin ion chanell) consist of some heteroatoms >> due to the presence of the non standart aminoacids in sequence: FOR, DLE, >> DVA, ETA ( this the R isomers instad of L analogs) >> >> >> I've tried to parametriesed that structure via different force fields but >> in all cases there are not suitable topologies for that aminoacids >> >> e.g >> Fatal error: >> Residue 'FOR' not found in residue topology database >> >> How I can solve that problem? I've tried to look for the suitable itp file >> but could not find it too :( >> > > For new protein residues, you do not need an .itp file, you need a suitable > .rtp entry such that pdb2gmx can incorporate it into your topology. > > http://www.gromacs.org/**Documentation/How-tos/**Parameterization<http://www.gromacs.org/Documentation/How-tos/Parameterization> > http://www.gromacs.org/**Documentation/How-tos/Adding_** > a_Residue_to_a_Force_Field<http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field> > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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