[gmx-users] the ligand have more than one molecules
Mark.Abraham at anu.edu.au
Sun Apr 17 11:31:26 CEST 2011
On 17/04/2011 7:05 PM, ahmet yıldırım wrote:
> 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?
A molecule .itp file can contain the [moleculetype] for that molecule.
It has a name given to it inside the [moleculetype]. This molecule is
replicated by grompp according to the number assigned next to the
reference to the name in the [molecules] section.
Your .top file could look something like this.
Read the examples in chapter 5, do some tutorials without trying to
modify them, and you will better understand the forms that .top files
> 16 Nisan 2011 02:08 tarihinde Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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 <http://vt.edu> | (540) 231-9080
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> Ahmet YILDIRIM
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