thanks justin actually i want to know that how these values of column (atom name, type, charge and charge group) we obtain for oxygen bonded with heme fe. is there any program through which i find the parameter file for oxygen with heme and nitric oxide with heme iron. if i just add the atom name type and charge in the bonded type heme fe atoms is it work for me can you tell me about any tutorial in which adding residue shows with examples that will be very understandable. thanks
On Wed, Jun 14, 2017 at 4:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/14/17 12:25 AM, Rana Rehan Khalid wrote: > >> Hi >> I have read the chapter 5 of manual but i am confuse how can i add residue >> into heme atom of .rtp ff >> this is the coordinate due to which error come >> >> HETATM 1529 O01 HEM 187 3.996 19.101 70.594 0.00 >> 0.00 O >> >> kindly guide me how i can make changes in the rtp file and .atp so that >> this error remove >> here is the heme rtp part of my selected ff where i can add O01 and also >> tell me these 4 column and these values and tell me which value i add for >> O01 like (FE FE 0.40000 0 ) >> > > You should refer back to the manual if the contents of these files are not > clear. You're seeking to introduce new parameters for an oxygen-bound form > of heme; this may require very complex parametrization work. Modifying an > .rtp file is trivial; it's just text. Putting realistic parameters into it > is a whole other matter. Check the literature for any existing efforts to > avoid duplicated work. > > -Justin > > [ HEME ] >> [ atoms ] >> FE FE 0.40000 0 >> NA NR -0.10000 0 >> NB NR -0.10000 0 >> NC NR -0.10000 0 >> ND NR -0.10000 0 >> CHA C -0.10000 1 >> HHA HC 0.10000 1 >> C1A C 0.00000 2 >> C2A C 0.00000 2 >> C3A C 0.00000 2 >> C4A C 0.00000 2 >> CMA CH3 0.00000 3 >> CAA CH2 0.00000 4 >> CBA CH2 0.00000 4 >> CGA C 0.27000 5 >> O1A OM -0.63500 5 >> O2A OM -0.63500 5 >> CHB C -0.10000 6 >> HHB HC 0.10000 6 >> C1B C 0.00000 7 >> C2B C 0.00000 7 >> C3B C 0.00000 7 >> C4B C 0.00000 7 >> CMB CH3 0.00000 8 >> CAB CR1 0.00000 9 >> CBB CH2 0.00000 9 >> CHC C -0.10000 10 >> HHC HC 0.10000 10 >> C1C C 0.00000 11 >> C2C C 0.00000 11 >> C3C C 0.00000 11 >> C4C C 0.00000 11 >> CMC CH3 0.00000 12 >> CAC CR1 0.00000 13 >> CBC CH2 0.00000 13 >> CHD C -0.10000 14 >> HHD HC 0.10000 14 >> C1D C 0.00000 15 >> C2D C 0.00000 15 >> C3D C 0.00000 15 >> C4D C 0.00000 15 >> CMD CH3 0.00000 16 >> CAD CH2 0.00000 17 >> CBD CH2 0.00000 17 >> CGD C 0.27000 18 >> O1D OM -0.63500 18 >> O2D OM -0.63500 18 >> >> thanks >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
