AW: patch for cystein bond

From: Bernitzky, Cornelius Constantin Maria (
Date: Thu May 09 2019 - 03:48:07 CDT

Many thanks, it works now.

When I had kept the numbers of the DISU-patch it did not work for different reasons and I somehow thought, that the numbers are only needed if there are two residues of the same type... so Joshua made exactly the assumption that I needed.

Best wishes,

Cornelius Bernitzky

Von: Lennart Nilsson <>
Gesendet: Mittwoch, 8. Mai 2019 22:10
An:; Brian Radak; Bernitzky, Cornelius Constantin Maria
Betreff: RE: namd-l: patch for cystein bond

Brian is right - please do read the documentation. The IC table does NOT create any energy terms (bonds, angles, etc).
For some reason you removed the all-important digits in front of the atom names.... They indicate which residue the atom belongs to, and without them all atoms are supposed to be in the same residue.

Best wishes,
Lennart Nilsson

From: [] On Behalf Of Brian Radak
Sent: den 8 maj 2019 20:15
To: namd-l <>; Bernitzky, Cornelius Constantin Maria <>
Subject: Re: namd-l: patch for cystein bond

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 <<>> 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?
    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 (

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

När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<>.

Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<>.

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:20:46 CST