[gmx-users] the ligand have more than one molecules

[ahmet yıldırım]

Dear Justin,

I have 6 EDO and 1 TRS ligans. I created coordinate and .itp files for each
EDO molecule using prodrg web server. I am adding coordinates of each EDO
molecule into a file called conf.gro. The conf.gro file is obtained from
without_EDO_TRS. pdb ( there is not ligands). is this procedure correct?

I do not know what to do about EDO.itp because .itp files obtained from the
prodrg web server are the same. How can I create one .itp file for all the EDO
molecules?

Thanks


16 Nisan 2011 02:08 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:

>
>
> ahmet yıldırım wrote:
>
>> Dear users,
>>
>> Is there anyone has a tutorial of the ligand have more than one molecules?
>>
>
> Perhaps you can describe in more detail what it is you hope to accomplish.
>  The procedure for dealing with multiple ligands is, in principle, no
> different from a single ligand.  There are not tutorials available for every
> variation of a procedure.
>
> -Justin
>
>
>  For example:
>> *_topol.top:_*
>> [ molecules ]
>> ; Compound        #mols
>> Protein_chain_A     1
>> Protein_chain_B     1
>> *ligandname  *         3
>>
>> Thanks in advance
>> --
>> Ahmet YILDIRIM
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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-- 
Ahmet YILDIRIM
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