Hello Yuan-- > I wonder if there is an example for proper topology and parameter treatment > for > phosphorylated-serine residue available that works with the protein_1.0.top > and > protein_1.0.par files that come with xplor-nih-2.37? I have examples from > other > sources but the charges/distances etc. are treated slightly different overall > from the above two files.
The approach we have which should work out of the box with Xplor-NIH
is to use the SP patch to convert a serine into phosphoserine:
xplor.command("patch SP refe=1=(resid XX) refe=2=(resid YY)
where XX is the resid of the serine, and YY is the resid of a
separately initialized phosphate group. Please see
eginput/PSF_generation/genModCircPep.py
for a worked-out example. For this usage, you will want to write out
the PSF and work with this. A more convenient patch could be written,
or a separate residue type could be introduced.
>
> Also I saw that there are examples for protein-DNA complex and prot-prot
> docking
> in the /eginput folder. I wonder if there is also a protein-peptide example
> available? The prot-prot docking protocol relies much on the input structures,
> and I wanted to take into account more of the peptide flexibility. Much
> appreciation in advance for any help!
>
This does depend somewhat on what sort of data you have for the
calculation. The attached script (a modified version of
eginput/relaxRatio/dock_rrp.py from the Xplor-NIH distribution) might
be a place to start. You will have to carefully free the appropriate
regions of (presumably mostly) the peptide.
Please let me know if you have problems with this.
best regards--
Charles
dock.py
Description: Binary data
_______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
