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 <[EMAIL PROTECTED]> 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
========================================
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