[gmx-users] Assigning charge to closely related functional group

[Tushar Ranjan Moharana]

Hi All,
Following is the structure of the molecule, which I wish to parameterize.
         CH3      O
          |           ||
CH3 - C - O - C -
          |
         CH3
It is a peptide capping reagent. The last carbon will form bond with the
NH2 group of the peptide. I have generated the the topology using PRODRG
server and wish to refine the charge group and partial charges as PRODRG
server doen't predict them correctly. The closest well-validated structure
is of carboxyl ester in the first position of DPPC (or any other
glyceride). However there is a minor difference. The carbon attached to
three methyl group, in this case is CH0 type and in DPPC it was CH2 type.
Since the carbon was part of charge group in DPPC, I fear I may have to
change the partial charges. I couldn't find any example where exactly same
charge group was used. I will appreciate if anyone can suggest me how to
assign correct partial charges.

Thanks a lot for the help.


"A society with free knowledge is better than a society with free food"

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB