[gmx-users] the ligand have more than one molecules
ahmedo047 at gmail.com
Sun Apr 17 11:05:28 CEST 2011
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
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.
> For example:
>> [ 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
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