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

[Steven Neumann]

Maybe in other words:

Can I create dipol in my aminoscids.rtp file which will be positively
charged (+1) - NH+

[ POS ]
 [atoms]
    N       N       0.7     0
    H       H       0.3     1
 [bonds]
    N       H

Please, help whether this is not a mistake adding new residue with such
charges?

On Mon, Jan 23, 2012 at 9:31 AM, Steven Neumann <s.neumann08 at gmail.com>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...
>
> I will appreciate your response. Thank you!
>
> Steven
>
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