[gmx-users] PRODRG -cgnr
Atila Petrosian
atila.petrosian at gmail.com
Sun Jul 27 18:20:21 CEST 2014
Dear gromacs users
I wan to use PRODRG server to do md simulation of my system (drug-protein
complex).
I know charge and cgnr parameters obtained from PRODRG (for ligand
molecule) are not accurate.
I know there are 2 ways to solve this problem:
1) If there are special functional groups in my ligand, I can find theses
functional groups being in protein, DNA and RNA molecules. Then I can
reassign charges and charge groups from these moieties.
2) Another way is to get partial charges from QM calculation.
I have some questions about second way:
Since the topology (itp file) parameters obtained from PRODRG are based on
GROMOS force field, I should consider cgnr correctly.
For example, in ffG43A1, N and H atoms form one charge group (cgnr = 0),
thus, summation of these charges are zero (-0.280 + 0.280 = 0).
N N -0.280 0
H H 0.280 0
Using QM calulations, I can only obtain partial charges (mulliken charges).
My main question is that if I obtain partial charges using QM calulations,
how to set cgnrs?
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