[gmx-users] Define a new residue in oplsaa

[Justin A. Lemkul]

Shima Arasteh wrote:
> Dear GROMACS users,
> I wanna add add a FOR residue containing atom C and O. In oplsaa force 
> field, the most similar residue to formyl (FOR) is ACE.
> How I can change the ACE in .rtp file in oplsaa ff to define FOR residue 
> as a new residue?
> I did like this, Is it correct?
> 

No.  See below.

> [ ACE ]
>  [ atoms ]
>    CH3    opls_135   -0.180     1
>   HH31    opls_140    0.060     1
>   HH32    opls_140    0.060     1
>   HH33    opls_140    0.060     1
>      C    opls_235    0.500     2
>      O    opls_236   -0.500     2
>  [ bonds ]
>    CH3  HH31
>    CH3  HH32
>    CH3  HH33
>    CH3     C
>      C     O
> [ impropers ]
>   CH3    +N    C      O     improper_O_C_X_Y
> 
> [ FOR ]
>  [ atoms ]
>   HH31    opls_140    0.060     1
>   HH32    opls_140    0.060     1
>   HH33    opls_140    0.060     1

A formyl group has only one H atom, since it is an aldehyde.

>      C    opls_235    0.500     2
>      O    opls_236   -0.500     2

The charges here for C, H, and O will likely have to be recalculated.  See:

http://www.gromacs.org/Documentation/How-tos/Parameterization
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

>  [ bonds ]
>      C     O

You need a C-H bond as well.

> [ impropers ]
>   CH3    +N    C      O     improper_O_C_X_Y
> 

There is no CH3 in a formyl group.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
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

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