Hi,
Can you change the atom name from PTR to Y1P as specified in the parameter
file and try?
Soumya
**
**
On Mon, Dec 19, 2011 at 2:49 PM, Sangeetha B <sangeetha.bicpu.edu.in> wrote:
> 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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> > AMBER.ambermd.org
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>
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Received on Mon Dec 19 2011 - 02:00:03 PST
