[gmx-users] #include "ffG45a3.itp"

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> Hi
> The same question is here. Would you please explain this again for me?
> Thank you
> Lin
> 
> 
> 2. the complete data for ffG45a3 are as follows
>  If I simply write "#include "ffG45a3.itp" in my .top file and do NOT
>  include others. Will Gromacs include all of the OTHERS automatically?
> Or, I  have to include all of them in my .top file.
> 
> 
> 
>  ffG45a3.itp
>  ffG45a3.ddb
>  ffG45a3.hdb
>  ffG45a3.rtp
>  ffG45a3bon.itp
>  ffG45a3nb.itp
>  ffG45a3-c.tdb
>  ffG45a3-n.tdb
>  ffG45a3.atp
> 
> 

Most of this information is used by pdb2gmx - rtp, tdb, hdb, atp - in forming 
the topology.  Calling #include "ffG45a3.itp" calls the parameters from the 
ffG45a3bon.itp and ffG45a3nb.itp files.

I suggest a thorough look through Chapter 5 of the manual to understand how all 
of this works.

-Justin

> 
> 
> Chih-Ying Lin wrote:
>> HI
>> 1. when i make a .top file myself, i wrote the command #include "ffG45a3.itp".
>> with this command, does it mean that Gromacs will assign the force
>> field parameters automatically for those I do NOT write into the .top
>> file ?
>>
>>
> yes, if they are present in the FF.
> 
>> 2. the complete data for ffG45a3 are as follows
>> If I simply write "#include "ffG45a3.itp" in my .top file and do NOT
>> include others automatically. Or, I have to include all of them in my
>> .top file.
>>
> No.
> 
> 
>> Thank you
>>
>> Lin
>>
>> ffG45a3.itp
>> ffG45a3.ddb
>> ffG45a3.hdb
>> ffG45a3.rtp
>> ffG45a3bon.itp
>> ffG45a3nb.itp
>> ffG45a3-c.tdb
>> ffG45a3-n.tdb
>> ffG45a3.atp
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> 
> 
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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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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