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

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> Molecular Dynamics wrote:
>> 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 
> 
> 1. If you are using the original PRODRG, don't.  The parameters it 
> generates are for ffgmx, which is deprecated and should not be used.  
> Use PRODRG-2.5 (beta server) and get a Gromos96 43a1-compatible topology.
> 2. The charges and charge groups assigned by PRODRG are inconsistent, at 
> best. You will need to consult the manual for information about charge 
> groups, and existing elements of the force field to determine whether or 
> not the charges assigned are appropriate.
> 

I should also add to this that just because you assign what you believe are 
reasonable parameters, does not mean they will necessarily be valid.  You must 
validate the parameters appropriately.  For Gromos96, this will involve 
measurements of thermodynamic variables and experimental observables.  Refer to 
the literature regarding the force field.  Parameterization is a time-consuming 
process.  While PRODRG does a nice job of automating topology construction, it 
is the task of the user to actually verify the applicability of the parameters.

-Justin

>> 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 
> 
> I'm not sure I fully understand.  You will obviously have to re-name the 
> files to have them make any sense.  You also cannot call both of them 
> "DRG" within the .pdb and .itp files, as is the output of PRODRG.
> 
>> 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 ?
> 
> Using genbox should be fine.
> 
> -Justin
> 
>>  
>> 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 <http://vt.edu/> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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>>
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>>
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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

========================================