Hi,
Thanks for your suggestion. Actually, i changed the atom types in my
protein to be consistent with the one in the parameter file before
loading into leap. The atom types seems to be fine in the pdb file
that i save along with the prmtop and inpcrd. But in the pdb file that
i extract using ambpdb and rst after minimization, the atom types
seems to change.
Phosphotyrosine before minimization (during prmtop generation)
ATOM 2803 N PTR 176 -24.278 -13.878 5.811 1.00 0.00
ATOM 2804 H PTR 176 -24.526 -13.065 5.292 1.00 0.00
ATOM 2805 CA PTR 176 -22.895 -14.368 5.691 1.00 0.00
ATOM 2806 HA PTR 176 -22.752 -15.200 6.365 1.00 0.00
ATOM 2807 CB PTR 176 -22.651 -14.747 4.222 1.00 0.00
ATOM 2808 HB2 PTR 176 -22.556 -13.832 3.647 1.00 0.00
ATOM 2809 HB3 PTR 176 -21.694 -15.255 4.159 1.00 0.00
ATOM 2810 CG PTR 176 -23.727 -15.644 3.629 1.00 0.00
ATOM 2811 CD1 PTR 176 -24.307 -16.695 4.346 1.00 0.00
ATOM 2812 HD1 PTR 176 -24.011 -16.885 5.367 1.00 0.00
ATOM 2813 CE1 PTR 176 -25.253 -17.526 3.762 1.00 0.00
ATOM 2814 HE1 PTR 176 -25.694 -18.340 4.304 1.00 0.00
ATOM 2815 CZ PTR 176 -25.635 -17.322 2.451 1.00 0.00
ATOM 2816 CE2 PTR 176 -25.112 -16.249 1.724 1.00 0.00
ATOM 2817 HE2 PTR 176 -25.440 -16.075 0.716 1.00 0.00
ATOM 2818 CD2 PTR 176 -24.161 -15.429 2.323 1.00 0.00
ATOM 2819 HD2 PTR 176 -23.741 -14.614 1.758 1.00 0.00
ATOM 2820 OG PTR 176 -26.573 -18.228 1.901 1.00 0.00
ATOM 2821 P PTR 176 -26.111 -19.607 1.309 1.00 0.00
ATOM 2822 O1P PTR 176 -24.891 -19.202 0.407 1.00 0.00
ATOM 2823 O2P PTR 176 -25.784 -20.545 2.498 1.00 0.00
ATOM 2824 O3P PTR 176 -27.312 -20.173 0.516 1.00 0.00
ATOM 2825 H1P PTR 176 -25.216 -19.072 -0.474 1.00 0.00
ATOM 2826 C PTR 176 -21.864 -13.322 6.192 1.00 0.00
ATOM 2827 O PTR 176 -20.638 -13.405 5.997 1.00 0.00
Phosphotyrosine after minimization
ATOM 2804 H PTR 176 17.814 22.540 49.089 1.00 0.00 H
ATOM 2805 CA PTR 176 19.616 21.488 49.442 1.00 0.00 C
ATOM 2806 HA PTR 176 19.810 20.495 49.847 1.00 0.00 H
ATOM 2807 CB PTR 176 19.792 21.414 47.919 1.00 0.00 C
ATOM 2808 HB2 PTR 176 19.736 22.424 47.512 1.00 0.00 H
ATOM 2809 HB3 PTR 176 20.787 21.026 47.702 1.00 0.00 H
ATOM 2810 CG PTR 176 18.768 20.554 47.207 1.00 0.00 C
ATOM 2811 CD1 PTR 176 18.946 19.162 47.102 1.00 0.00 C
ATOM 2812 HD1 PTR 176 19.819 18.703 47.540 1.00 0.00 H
ATOM 2813 CE1 PTR 176 17.987 18.372 46.429 1.00 0.00 C
ATOM 2814 HE1 PTR 176 18.137 17.306 46.373 1.00 0.00 H
ATOM 2815 CZ PTR 176 16.845 18.977 45.832 1.00 0.00 C
ATOM 2816 CE2 PTR 176 16.674 20.372 45.974 1.00 0.00 C
ATOM 2817 HE2 PTR 176 15.799 20.841 45.546 1.00 0.00 H
ATOM 2818 CD2 PTR 176 17.620 21.152 46.662 1.00 0.00 C
ATOM 2819 HD2 PTR 176 17.456 22.213 46.777 1.00 0.00 H
ATOM 2820 OG PTR 176 15.929 18.365 45.100 1.00 0.00 O
ATOM 2821 P PTR 176 15.910 16.814 44.752 1.00 0.00 P
ATOM 2822 OP1 PTR 176 17.316 16.530 44.082 1.00 0.00 O
ATOM 2823 OP2 PTR 176 15.815 16.001 45.975 1.00 0.00 O
ATOM 2824 O3P PTR 176 14.916 16.631 43.672 1.00 0.00 O
ATOM 2825 H1P PTR 176 17.432 17.225 43.437 1.00 0.00 H
ATOM 2826 C PTR 176 20.621 22.479 50.094 1.00 0.00 C
ATOM 2827 O PTR 176 21.837 22.268 50.028 1.00 0.00 O
On Mon, Dec 19, 2011 at 2:31 PM, Soumya Lipsa Rath
<soumyalipsabt.gmail.com> wrote:
>
> Hi,
>
> Have you checked the atom type present in the pdb file and the parameter
> file for your phosphotyrosine residue? As I can see from the picture the
> atoom types are OG, OP1, OP2, O3P which doesn't look consistent.
>
> Soumya
>
> On Mon, Dec 19, 2011 at 2:11 PM, Sangeetha B <sangeetha.bicpu.edu.in> wrote:
>
> > Hi,
> >
> > 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.
> >
> > The input I used for minimization is given below:
> >
> > complex: initial minimisation solvent + ions
> > &cntrl
> > imin = 1,
> > maxcyc = 5000,
> > ncyc = 2500,
> > ntpr = 25,
> > cut = 10.0,
> > /
> >
> > It will be very helpful if any one can tell me what is the reason for this
> > problem. Any suggestions regarding this would be helpful.
> >
> >
> > with regards,
> >
> > Sangeetha
> > Research Scholar
> > Centre for Bioinformatics
> > Pondicherry University
> > Pondicherry
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> _______________________________________________
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Received on Mon Dec 19 2011 - 01:30:03 PST
