[gmx-users] Topology files

[kirtana S]

For example if I have a polystyrene polymer chains and monomers of user
defined solvent . I need to construct the .itp file by hand .

Thanks for the reply
Kirtana

On Tue, Feb 28, 2012 at 5:31 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> kirtana S wrote:
>
>> Dear Users,
>>
>> In the gromacs manual on means to convert the pdb file to gromacs
>> topology file I need to use pdb2gmx. Here I have to specify the force field
>> .How to work with organic residues which do not exists . Since I had used
>> general amber force field, and could not find this in the /share/top/
>> directory . Do I need to manually construct the .itp file for each
>> residues. What will be the easiest way to construct
>> a solvated box with user defined residues in gromacs.
>>
>>
> If the residue of interest will be a component of a polymeric molecule
> like a protein, refer to http://www.gromacs.org/**
> Documentation/How-tos/Adding_**a_Residue_to_a_Force_Field<http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field>.
>  If the molecule is a standalone species like a ligand, solvent, etc then
> all you have to do is #include an .itp file in the system topology.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
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> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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