I tried to simulate a 3 residue peptide with Y1P as the second
residue, also another simulation for the Y1P alone obtained from the
parameter file. In all these simulations I got the same problem.
Sangeetha
On Mon, Dec 19, 2011 at 3:18 PM, Soumya Lipsa Rath
<soumyalipsabt.gmail.com> wrote:
> 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
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>> > >
>> > >
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Received on Mon Dec 19 2011 - 04:00:03 PST
