Re: HEME and Cystein instead of His

From: Raul Araya (arayasecchi_at_gmail.com)
Date: Wed Nov 23 2011 - 14:25:37 CST

Aron

Thanks for your answer...that is exactly what Im triying to do and in fact
I already found some usefull patch to link a Cys to the HEME group.
However, ther is another thing that I´m interested to learn how to do:

I want to link an Oxygen atom double-bonded to the FE atom in the HEME
group together with the CYS as described in: PROTEINS 64:147(2006) and in J
Mol Graph Mod 30:1(2011). There is a patch called PLO2 in the charmm
topology file but intended to link a O2 molecule to the HEME group.

Again, any help will be most appreciated....

Raúl Araya Secchi
B.Sc Molecular Biotechnology.
Molecular Biotechnology Engineer.
PhD Student (Biotechnology Program. UNAB, Chile)
Computational Biology Lab (DLab)
Center for Mathematical Modeling (CMM)
Facultad de Ciencias Físicas y Matemáticas.
Universidad de Chile.

2011/11/23 Aron Broom <broomsday_at_gmail.com>

> I've previously made new molecules for CHARMM. I don't know if they
> formats have changed, but it used to be that the topology and parameter
> files were human readable. If this is the case, you could just take your
> HEME-His definition and change it around to be HEME-Cys. Obviously you
> might need to consider the various parameters for the atoms under this new
> environment, maybe using a higher level of theory.
>
> In terms of autopsfgen I'm not sure what the intended usage method is, but
> you stick your new HEME-Cys topology and parameters inside the existing
> topology and parameter files and rename them, you can pass those topology
> and parameter files to autopsfgen and it will work fine.
>
> ~Aron
>
>
> On Wed, Nov 23, 2011 at 2:10 PM, Raul Araya <arayasecchi_at_gmail.com> wrote:
>
>> Dear NAMD users
>>
>> Im interested in simulating a cytochrome protein whos HEME group is
>> linked to a CYS residue and not to a HIS.
>> I have found on the CHARMM topology files patches for linkinf the HEME
>> group to a HIS...
>>
>> Does anybody nows or have the patch to link the HEME to a CYS?
>>
>> I heard about a patch called FE2S that is supposed to link the HEME to a
>> CYS but I have not been able to find it....
>>
>> How are the other HEME related patches used with autopsfgen?
>>
>> Any help will be appreciated.
>>
>>
>> Raúl Araya Secchi
>> B.Sc Molecular Biotechnology.
>> Molecular Biotechnology Engineer.
>> PhD Student (Biotechnology Program. UNAB, Chile)
>> Computational Biology Lab (DLab)
>> Center for Mathematical Modeling (CMM)
>> Facultad de Ciencias Físicas y Matemáticas.
>> Universidad de Chile.
>>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:34 CST