RE: patch for cystein bond

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed May 08 2019 - 13:37:31 CDT

Ok, I'm going to make some assumptions here about the gold structure in the psf. Basically, the patch command needs to be told where the modifications are being made. If you just say something like:

patch AUST P:41

That will modify residue 41 of segment P by the given patch. Since residue 41 of that segment likely does not include any gold atoms, psfgen/charmm will add those new atoms in. What you want is likely something like this:

PRES AUST -0.36 ! patch for CYS on gold surface
                                       ! use in a patch statement
                                       ! follow with AUTOgenerate ANGLes DIHEdrals command?
    GROUP
    ATOM 1CB CT2 -0.10 ! | .
    ATOM 1SG SM -0.08 ! HN-N .
    GROUP ! | HB1 .
    ATOM 2A12 AU -0.08 ! | | A11
                                            ! HA-CA--CB--SG--A12
                                            ! | | A13
                                            ! | HB2 .
                                            ! O=C .
    DELETE ATOM HG1 ! | .
BOND 1SG 2A12

And then calling the patch command like so:

patch AUST P:41 GS:1 ; #This assumes that your gold surface has one residue and is in segment GS

The important part here are the numbers in front of the atom names in the patch. These indicate which of the residues passed in the patch line each atom belongs to.

-Josh

On 2019-05-08 08:34:37-06:00 owner-namd-l_at_ks.uiuc.edu 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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