[gmx-users] Help: A ligand covalently bond to protein

[Yang Ye]

for more features like angle or dihedral, merge each section of their 
itp (offset all the numbers in the second itp for an offset) shall be a 
more elegant way.

On 11/7/2007 6:00 AM, Tanping Li wrote:
> Dear Yang,
>
> Really thanks for the help. Distance constraint can
> describe the bond length between ligand and protein,
> how about other propery of covalent bond? Maybe I
> missed something of your message.
>
> Yours
> Tanping
>
>
> --- Yang Ye <leafyoung at yahoo.com> wrote:
>
>   
>> you might want to try distance constraint.
>>
>> On 11/7/2007 5:11 AM, Tanping Li wrote:
>>     
>>> Dear all,
>>>
>>> I searched the mailling list, and still can't find
>>>       
>> a
>>     
>>> way to set up my system: a ligand covalently bond
>>>       
>> to
>>     
>>> protein.
>>>
>>> I don't know if there is a easier way to do this.
>>>       
>> What
>>     
>>> I can think of is:
>>>
>>>
>>> 1) Add a bond I like in the specbond.dat file;
>>> 2) Add a block for ligand in the rtp file;
>>> 3) run pdb2gmx, gromacs will treat protein and
>>>       
>> ligand
>>     
>>> a one chain since it can see the bond in the
>>> specbond.dat.
>>>
>>>
>>> I just wonder if there is a eaiser way to add a
>>>       
>> ligand
>>     
>>> to rtp file? When I run Dundee PRODRG2, I get a
>>>       
>> .itp
>>     
>>> file. Is there some way to change this into rtp
>>> format? It is not trival to write a rtp manually.
>>> Really appretiate your help.
>>>
>>> Yours
>>> Tanping
>>>
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