[gmx-users] Re: #include "ffXXX.itp"

[Justin A. Lemkul]

Chih-Ying Lin wrote:

> so,
> [bonds]
> ; ai  aj  funct
> 8     9     gb_28
> is correct.......
> 
>

No.  The function type is not the same as a bond type.  Read in Chapter 5 about 
the difference.  If you have atoms 8 and 9 as a bond, with the appropriate 
function type, the grompp will assign the values associated with gb_28 to that bond.


> [bonds]
> ; ai  aj  funct
> 8     9
> is INCORECT.......  and 8 , 9 will NOT be automatically bonded,  right?
> 

Right, that is *also* incorrect.

Perhaps it would be beneficial for you to run through some tutorials with simple 
proteins to see topologies that are automatically generated and how they work.

-Justin

> The same for the nonbonded parts, right?
> Thank you
> Lin
> 
> 
> 
> 
> 
> 
> 
> 
> On 9/22/08, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>>  Chih-Ying Lin wrote:
>>
>>> HI
>>>
>>>  The command
>>>  #include "ffXXX.itp" is putting in the .top file.
>>>
>>>  How does this command automatically assign the force field
>>>  parameters which I did not assign in my .top file?
>>>
>>>  Is it based on the atom types which I assign in my .top file?
>>>  Then, all the force field parameters from "include ffXXX.itp"  will
>>> give the both bonded
>>>  and non-bonded parameters according the atom types, right?
>>>
>>>
>>> I mean...... once I determine the atom type.......such as NL and CH3......
>>> there is a bond between NL and CH3.....
>>> But i did not assign the bond parameters in my .top file while I add
>>> the command
>>> "#include "ffXXX.itp" in my .top file.
>>>
>>> Will this command #include "ffXXX.itp" automatically assign a bond
>>> parameter for it?
>>>
>>>
>>>
>>  Yes, as long as those atoms are listed as bonded within the [ bonds ]
>> section of your .top file.
>>
>>
>>> Other than this, there are so many non-bonded force field parameters.
>>> Once, I determine the atom types such as O and CR1.
>>> But, I did not assign any non-bonded parameters for them in my .top file.
>>> Will this command  #include "ffXXX.itp" assign all the non-bonded
>>> force field parameters for me based on the atom types automatically?
>>>
>>>
>>  Yes.
>>
>>  -Justin
>>
>>
>>> Thank you
>>> Lin
>>>
>>>
>>  --
>>  ========================================
>>
>>  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
>>
>>  ========================================
>>
> 

-- 
========================================

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

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