[gmx-users] using more than one type of molecules

[Molecular Dynamics]

Dear Justin,

I use DRGGMX.ITP and DRGPOH.PDB for each type of molecule from the PRODRG. And you suggested that ' If these come from PRODRG, they will probably require manual modification and validation of their contents.' What kind of modifications should I do ? Could you please give me some info about it ? And I 'm planning to obtain a binary mixture ( X : 120 Y : 60 molecules number for example ) . According to your suggestions I will have used DRGGMX.ITP and DRGPOH.PDB  files of  X molecule, but I will just have used DRGGMX.ITP file of Y molecule. Isn't it important to use DRGPOH.PDB  file of Y molecule. Because Y is not a solvent. X and Y are organic molecules. And I think this is the unique way to obtain a binary mixture with using –cp X.pdb –cs Y.pdb in Gromacs usage. Could you explain these significant issues ? 

Sincerely




________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Friday, March 13, 2009 8:25:14 PM
Subject: Re: [gmx-users] using more than one type of molecules



Molecular Dynamics wrote:
> 
> 
> Dear All,
> 
> 
> I'm new to Gromacs and have some questions to learn the answers. I study on one type molecule. If I want to add lets say 240 molecules, which is the best way to use editconf or genbox ? And I learned the procedure of using more than one type of molecules in gromacs. But I'm not sure, so I'm waiting for your contributions. Assume that I have two small organic 

In general, the topol.top should consist of the #include statements for each .itp file, then the [ system ] directive should contain a count of each molecule.

Use editconf to set your box size, and genbox -ci -nmol to insert what you need.

> molecules like hydrocarbons X and Y. I think First I will have to get seperately DRGGMX.ITP and DRGPOH..PDB for the each molecules in different 

If these come from PRODRG, they will probably require manual modification and validation of their contents.

> work directories. Then chose one directory ( X ) and do the operations like in ''GROMACS Tutorial for Drug – Enzyme Complex'' Then in this command
> 
> 
> genbox –cp X.pdb –cs Y.pdb –o gmx.pdb –p gmx.top
> 
> 

If you are using X as the solute and Y as the solvent, then yes, this is fine. It is just like solvating a protein in water (if X = protein, Y = water).

> After I get gmx.pdb gmx.top files I will add #include “Y.itp” and editing the number of Y molecule and go on ..
> 

Correct.

-Justin

> 
> Could you please help me to learn the true process of using more than one type of molecules in gromacs ?
> 
> 
> 
> Sincerely
> 
> 
> 
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-- ========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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