Re: [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 <jalem...@vt.edu 
<mailto:jalem...@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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