Hi,
Just a note regarding OP1,OP2,O3P naming: this happens upon writing a pdb
with ambpdb. I presume the name is O1P, O2P, O3P in the prmtop. When you
write a pdb with ptraj, the names from the prmtop will be used.
Marc
On 19 December 2011 09:01, 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
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
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Received on Mon Dec 19 2011 - 02:00:03 PST
