patch for cystein bond

From: Bernitzky, Cornelius Constantin Maria (cornelius.bernitzky_at_campus.tu-berlin.de)
Date: Wed May 08 2019 - 09:28:01 CDT

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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