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

[Mark Abraham]

On 23/01/2012 8:31 PM, Steven Neumann wrote:
> 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 (hydrophilic).
> 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...

Since you'll need strong position restraints to keep your artificial 
surface intact, and have a heavy burden of proof that you have a valid 
model of something even without inventing partial charges for positive 
fragments, go ahead and invent anything you think might work... :-) The 
requirement of 3-atom fragments seems unduly restrictive.

Mark