Justin, It's not quite understood for me why such errors occurs in the atoms of standard residues when I've bounded them to the C term of my chromophore if the geometry of the adjacent residues might not be changed. So it likely that some errors occur during parametrization of the molecule which I could not identify ( In any case I'll be very thankful for anyone who can provideme with some other version of the integrated chromophore in charm for my future effort-on-errors :) The main problems which I've forced in the improper group definition ( I've not recognize in the paper of simulation in charmm22 what groups should define as improper although Swiss param produce the big set of such groups- see below )
In addition It'll be very hardly to connect chromophore with adjacent residues mainly due to definition of the addition dihedrals. Finally Im not quite sure about CMAP definition ( I've used C NH1 CT1 C NH1 1 24 24\ C NH1 CT1 C N 1 24 24\ in the CMAP.itp with the atom names of chromophore C NH1 CT1 C NC=O 1 24 24\ C NC=O CR C=O N=C 1 24 24\ C=C C=O NC=O CR C=O 1 24 24\ C=O NH1 CT1 C NH1 1 24 24\ where NC=O and N=C types correspond to the N and CR is the C-alpha atoms James 2012/12/15, Justin Lemkul <[email protected]>: > > > On 12/15/12 2:18 PM, James Starlight wrote: >> So as I understood it've happened because the conformation of the >> adjacent residue is differ when that residue bounded to the >> chromophore ( in comparison to the residue in unbound capped form). > > Conformation is irrelevant; atom types are all that matter here. > >> But in term of the backbone geometry of C and N-terms chromophore is >> like a typical amino acid. Also Chromophore is defined as a protein in >> the residue.dat. When I've examined error log of my system I've >> noticed that missing UB and dihedral parametrs of the i+1 residue have >> never present in the ffbounded.itp ( the exact combination of the >> triplet and quadruplet of atoms for UB and dihedral). Is there any >> other ways to define termi of my non standard residue as the standard >> one? >> > > If a particular bonded interaction is not present in the parent force field, > you > have to derive it parameters for it. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
