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-- Sangeetha On Mon, Dec 19, 2011 at 6:44 PM, David A Case <case.biomaps.rutgers.edu> wrote: > On Mon, Dec 19, 2011, Sangeetha B wrote: >> >> I am simulating a protein which contains two phosphotyrosine residues using >> Amber 11 and ff99SB force field. >> For the parameters of Phosphotyrosine with single protonated phosphate >> group, i used the ones available at >> http://www.pharmacy.manchester.ac.uk/bryce/amber >> The structure obtained after 1000 cycles of minimization showed some >> connectivity problem in the phosphate group. An image showing the lack of >> connectivity between one of the phosphate oxygens is attached with this >> mail. > > You don't say how the image was made, but most molecule viewing programs draw > bonds based on assumptions about distances between atoms. You might want to > compare the four O-P bond lengths in the minimized structure. > > If you use VMD, and load the prmtop file first, then VMD will use the > bonds in the prmtop file to decide which bonds to draw on screen. Other > programs may have similar options. You can also use rdparm to print a > list of the bonds in your system; in any event, these don't change upon > minimization. > > I agree that it is odd that the atom names (not atom types, which are not > present a pdb file) are OP1, OP2 and O3P. But you can probably track that > down somehow. > > ...dac > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Dec 19 2011 - 20:00:02 PST