[gmx-users] Partial charges of new RES in Charmm

Steven Neumann s.neumann08 at gmail.com
Mon Jan 23 10:31:08 CET 2012

Hi Gmx Users,

I am building a surface as a reperesentation of protein surface. In this
case I divide amino acids as: polar, nonpolar, positively charged and
negatively charged. Representation of 3 atoms constitutes one residue. I
created new residues (Charmm27) using exsiting charges:

e.g. Residue  - Negative [ NEG ]

[ NEG ]

[ atoms ]

CC       C        0.34          0

OT1     OC     -0.67         1

OT2      OC     -0.67       2

[ bonds ]

CC     OT1

CC     OT2
Theses charges are taken from COO- group of terminal residue [ GLY ]. I am
able to find partial charges for Hydrophobic  (CH2). However, I cannot find
for positive representation of 3 atoms) for positive or hydrophilic
residues. They always come as 2 or 4 atoms giving positive (+1) of neutral

My question: Can I create me own partial charges for given positive or
hydrophilic group? Is that ok for the force field? As different atoms in
different groups have different charges it should be fine in this case...

I will appreciate your response. Thank you!

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