[gmx-users] How to generate .itp file for a given molecule

[Tsjerk Wassenaar]

Hi,

Well, about .itp files. itp simply means "Include ToPology", i.e. a
file to be #include-d in a topology file. In most cases here on the
list it is used to designate a file which contains a [ moleculetype ]
description. The [ moleculetype ] is explained in detail in the manual
chapter 5. In short, it requires a listing of [ atoms ] (with masses,
charges, names and types) and, for molecules, also the following
directives:

[ bonds ]
[ pairs ]
[ angles ]
[ dihedrals ]

Possibly, you also want (maybe with an appropriate #ifdef .. #end)

[ position_restraints ]
[ distance_restraints ]
[ exclusions ]

Altogether, that will give you a topological description of of your
molecule which complements the coordinate information in the structure
file (.gro/.pdb).

Cheers,

Tsjerk

On Sat, Jul 12, 2008 at 12:15 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> DEEPESH AGARWAL wrote:
>>
>> Hi Prasun,
>>
>> Running 'pdb2gmx' command on the pdb file generates 'posre.itp' file
>> along with .top and .gro files.
>>
>
> ...with one caveat: the molecule you're looking to parameterize must be
> defined in an .rtp entry.  I suspect if one needs to generate an .itp file
> for a ligand, this will not be the case :)
>
> -Justin
>
>
>> Deepesh
>>
>>
>> On 7/12/08, prasun kumar <prasun30 at gmail.com> wrote:
>>>
>>> dear users,
>>> I am facing a problem in generating the .itp file for a molecule that i
>>> have
>>> created.can any one please tell me the procedure how to generate the .itp
>>> file.Is there any way?
>>> thanx in advance.
>>> waiting for your suggestions
>>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623