Hi everybody, I want to use pdb2gmx command to create a .gro file and a .top file for PAMAM whose repeat unit is amidoamine ( attached ).
/
---CH2--CH2--CO-NH-CH2-CH2-N (see the attached figure)
\
The atom N have two same branches with --CH2--. I write the rtp file for it
as follows:
[ atoms ]
C1 opls_245 -0.050 1
.........
[ bonds ]
C1 -N7
.......
C6 N7
N7 +C1
N7 +C1
It seems not work, which gives a wrong top structure. The question is how
can I deal with the two branches of N. Any suggestion is appreciated.
Thanks in advance.
--
wende
<<attachment: amidoamine.jpg>>
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