Re: [AMBER] Phosphotyrosine connectivity problem

From: Sangeetha B <>
Date: Tue, 20 Dec 2011 09:07:03 +0530


Thanks for all the useful suggestions. With your help I was able to
find out the problem.
As was pointed out, when I extract the pdb frames using ptraj there
are no connectivity issues and the atom names does not change.
The image that I showed was taken for the pdb file converted from rst
using ambpdb.
In the pdbs obtained using ambpdb, the atom names are changed and that
is why I was having those problems.

Thank you for the suggestions and quick replies. It helped me a lot.

On Mon, Dec 19, 2011 at 6:44 PM, David A Case <> 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
>> 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
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Received on Mon Dec 19 2011 - 20:00:02 PST
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