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