Re: Patch link

From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Mon Jul 11 2011 - 10:16:54 CDT

Hi,  Erik, thanks for your sugestion. It helps a lot.
I was able to write this patch?

PRES PCY1  0.0    ! Patch residues must be 1-CYS, 2-HEME.
DELETE ATOM HG1
BOND 1SG 2FE
ANGL 1SG 2FE 2NA
ANGL 1SG 2FE 2NB
ANGL 1SG 2FE 2NC
ANGL 1SG 2FE 2ND
ANGL 1CB 1SG 2FE

FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND FE - S IN PARAMETER FILES

I think once that I solved the FE-S bond problem, the program will ask for the angles...

Flavio

--- On Sun, 7/10/11, Erik Nordgren <nordgren_at_sas.upenn.edu> wrote:

From: Erik Nordgren <nordgren_at_sas.upenn.edu>
Subject: Re: namd-l: Patch link
To: "flavio seixas" <oivalf_nix_at_yahoo.com>, "NAMD Users List" <namd-l_at_ks.uiuc.edu>
Date: Sunday, July 10, 2011, 9:27 AM

Hi Flavio,

Here is what I have used, for connecting a heme iron to a MET sulfur:

PRES PHMS  0.0    ! Patch residues must be 1-MET, 2-HEME.
BOND 1SD  2FE
ANGL 1CE  1SD  2FE    1CG  1SD  2FE
ANGL 1SD  2FE  2NA    1SD  2FE  2NB    1SD  2FE  2NC    1SD  2FE  2ND

I suppose your patch for linking heme iron to CYS sulfur will be similar... hope it helps,
Erik

On Fri, Jul 8, 2011 at 3:11 PM, flavio seixas <oivalf_nix_at_yahoo.com> wrote:

-- 
C. Erik Nordgren, Ph.D.
Dept. of Chemistry
University of Pennsylvania

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