Re: pentacoordinate heme

From: grazia cottone (cottone_at_fisica.unipa.it)
Date: Tue Mar 08 2011 - 16:58:27 CST

Hi Flavio,
thanks.
 I did everything with PHEM and PLIG in case of 6-ligated heme, and I'm
running the oxy, all is working fine.
While for the the 5-ligated I used PHEME, but not PLIG of course. Now,
the Charmm ff presents the NPH-FE and NR2-FE bonds,
so as the NPH-FE-NPH and the NR2-FE-NPH angles, for the oxy form only.
According to Meuwly et al., Biophys Chem, 98, 2002,183-207, these
should be changed , to have the doming.
I was wondering if it exists a .par file which contains already these
changes:

6-ligated, in the charmm ff
NPH FE 270.200 1.9580
NR2 FE 65.000 2.2000
should be in the 5-ligated
NPH FE 270.200 2.1000
NR2 FE 65.000 2.1000

6-ligated in the charmm ff
NR2 FE NPH 50.000 90.0000
NPH FE NPH 14.390 90.0000
should be in the 5-ligated
NR2 FE NPH 50.000 107.0000
NPH FE NPH 80.000 90.0000

Thanks!
Grazia

flavio seixas ha scritto:
> Hi Grazia,
>
> It could help if you attach the heme parameter and topology files you are using.
> But normaly Charmm ff used by namd present the heme in deoxy state. You must to use a patche to bond it to proximal HIS (in both oxy and deoxy) and another patche to bond it to O2 in oxy state.
>
> Flavio
>
>
> --- On Sun, 3/6/11, grazia cottone <cottone_at_fisica.unipa.it> wrote:
>
>
>> From: grazia cottone <cottone_at_fisica.unipa.it>
>> Subject: namd-l: pentacoordinate heme
>> To: namd-l_at_ks.uiuc.edu
>> Date: Sunday, March 6, 2011, 3:43 PM
>> Hi All,
>> I need to simulate both deoxy- and 6-ligated heme states in
>> myoglobin.
>> The .prm files are designed for the 6-ligated state only,
>> so my question is how
>> do you model the heme doming in the deoxy state?
>>
>> Thanks
>> Grazia
>>
>> -- Grazia Cottone
>> School of Physics
>> College of Engineering, Mathematics and Physical Sciences
>> University College of Dublin
>> phone +353-1-716 1945
>> +353-1-716-1794
>> email grazia.cottone_at_ucd.ie
>>
>> Dipartimento di Fisica
>> Università di Palermo
>> phone +39-091 6234262
>> fax +39-091 6162461
>> email cottone_at_fisica.unipa.it
>> grazia.cottone_at_unipa.it
>>
>>
>>
>
>
>
>
>

-- 
Grazia Cottone
School of Physics
College of Engineering, Mathematics and Physical Sciences
University College of Dublin
phone +353-1-716 1945
      +353-1-716-1794
email grazia.cottone_at_ucd.ie
Dipartimento di Fisica
Università di Palermo
phone +39-091 6234262
fax   +39-091 6162461
email cottone_at_fisica.unipa.it
      grazia.cottone_at_unipa.it

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