[gmx-users] Hello

[Mark Abraham]

On 9/01/2012 6:54 PM, Nirmal Prasad wrote:
> Dear Mark,
>
> Thanks for responding.
>
> I am new to Gromacs.
>
> I am working on Cytochrome P 450 proteins, these proteins contain HEME group.
>
> For MD run should I prepare separate protein and HEME group topologies
> and reconstruct protein-HEME complex.  Is this procedure is correct or
> not.

A [moleculetype] cannot have covalent bonds with atoms outside itself. 
So whether your HEME group bonds covalently determines what can be found 
in a [moleculetype].

Mark

>
> nirmal
>
>
>
> On 1/9/12, Mark Abraham<Mark.Abraham at anu.edu.au>  wrote:
>> On 9/01/2012 6:42 PM, Nirmal Prasad wrote:
>>> Hello,
>>>
>>> I am working on Heme containing proteins, is it necessary to treat
>>> Heme group as Ligand.
>> What do you mean by "treating as a ligand"?
>>
>> Mark
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