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

[Mark Abraham]

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.

#include "whatever/forcefield.itp"
#include "whateverprotein.itp"
#include "trs.itp"
#include "edo.itp"
#include "somewater.itp"

[molecules]
Protein 1
EDO 6
TRS 1
SOL 23445

Read the examples in chapter 5, do some tutorials without trying to 
modify them, and you will better understand the forms that .top files 
can take.

Mark

>
> Thanks
>
>
> 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.
>
>     -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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>     -- 
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>
>
>
> -- 
> Ahmet YILDIRIM

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