VMD-L Mailing List

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Sun Jul 27 2008 - 04:14:20 CDT

i have created a vmd-script (along with modifications in top-file) to
make dityrosine cross-link between two segments.
if anyone interested, let me know.

On Sat, Jul 26, 2008 at 9:21 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> Assuming no one has done it before, you'd need to create a patch in the
> topology file by analogy to the DISU one. It should be pretty
> straightforward, at least to a first order approximation (adjusting things
> like charges though should be done with care). You might also have to
> define a bond and angle in the parameter file if they don't already exist
> for those atom types.
>
> The appendix of the NAMD tutorial and the Topology File and Parameterizing a
> Novel Residue Tutorials might be helpful as well.
> http://www.ks.uiuc.edu/Training/Tutorials/
>
> On Jul 26, 2008, at 5:47 PM, Roman Petrenko wrote:
>
>> Hello all,
>> have anyone ever created dityrosine links (like disulfide bonds, i.e.
>> between two TYR residues)? i know that psfgen must be used, just
>> hoping that someone have already done this.
>> --
>> Roman Petrenko.
>> Physics Department
>> University of Cincinnati
>
> 

-- 
Roman Petrenko.
Physics Department
University of Cincinnati