Re: patch for cystein bond

From: Brian Radak (brian.radak_at_gmail.com)
Date: Wed May 08 2019 - 13:15:27 CDT

As it stands, this seems to be a question for the CHARMM RTF documentation.

How, and with what program, are you applying this patch?

On Wed, May 8, 2019 at 10:30 AM Bernitzky, Cornelius Constantin Maria <
cornelius.bernitzky_at_campus.tu-berlin.de> wrote:

> Dear developers,
>
>
> I want to attach a cysteine to a gold-surface for NAMD-simulation, using a
> patch within the topology-file.
>
>
> The patch is as the following:
>
>
> PRES AUST -0.36 ! patch for CYS on gold surface
> ! use in a patch statement
> ! follow with AUTOgenerate ANGLes
> DIHEdrals command?
> GROUP
> ATOM CB CT2 -0.10 ! | .
> ATOM SG SM -0.08 ! HN-N .
> GROUP ! | HB1 .
> ATOM A12 AU -0.08 ! | | A11
> ATOM A13 AU -0.10 ! HA-CA--CB--SG--A12
> ! | | A13
> ! | HB2 .
> ! O=C .
> DELETE ATOM HG1 ! | .
> BOND SG A12
> DONOR SG A12
> IC CA CB SG A12 1.5584 109.0000 176.9600 114.20 2.45
> IC CB SG A12 A13 1.86 114.20 180.0000 90.0000 2.884
>
>
> I derived this from the working DISU-patch, but noticed that the patch do
> not use the existing gold surface.
>
> It creates two new Au atoms, where "A12" is bound to the Sulfur under
> usage of the given internal coordinates.
>
>
> As it is stated in the NAMD-tutorial (
> https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node24.html
> )
>
> the ATOM command within patches can refer to adding a new atom (as it
> happens here) or to the modifying of existing atoms (what happens in the
> DISU-patch and what is desired for my case too).
>
>
> Do you can think of an idea, how to make NAMD use the existing
> gold-surface instead of adding new Au?
>
> The gold is defined in a .pdb like this:
>
> ATOM 167 A11 AUR A 2 -58.558 -59.167 -52.227 1.00 0.00
> B AU
>
>
>
> Best wishes,
>
> C. Bernitzky
>
>
>

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