From: AnkiReddy katha (kathaankireddy_at_gmail.com)
Date: Thu May 07 2015 - 06:17:27 CDT
Dear NAMD users
In the following schematic, "1" is central atom and bonded to three atoms
(2, 3, 4).
3
|
1
/ \
2
I am using OPLS force field to simulate a chemical system using NAMD. I
prepared a parameter file in the CHARMM format , however i need a
clarification regarding the atoms sequence in an improper dihedral
For the schematic shown above, OPLS parameter file is listing the order of
atoms in the improper dihedral as "4 3 1 2"
If we use Topo guessimpropers, it is listing atoms in sequence as " 3 1 4
2"
I think CHARMM style lists, central atom (here atom "1") as the first ,
followed by other three.
Even though you are using OPLS force field, the sequence of the atoms
should be according to the CHARMM style if we are running simulations with
NAMD
Could you please write , what sequence we should use for the schematic
shown above in the CHARMM format. Once we know this, we can use Topo
addimproper command to prepare a psf file.
Thank you
Best Regards
Anki
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