Dear Aashish,
if I understood correctly you have an amino acid like moiety that is inserted into the residue chain via standard peptide bonds. Your approach is generally correct. However, you have to make sure that the blocking groups ACE and NME have a total charge of 0, and maybe you even would like to constrain the atomic charges of the peptide group elements of your residue to some amino acid-like ones.
-> You need to define charge constraints to ensure that your new residue has a total charge of -1 when the blocking groups are omitted.
(Please see the tutorials on the R.E.D. server pages and also consult the Amber tutorials for that.)
Best regards,
Anselm
________________________________________
Von: Aashish Bhatt <aashish.ph16221.inst.ac.in>
Gesendet: Montag, 2. Dezember 2019 08:04:21
An: AMBER Mailing List
Betreff: [AMBER] Charge distribution in molecule
Dear Amber user
I have been trying to prepare force field parameter for a molecule which is
covalently bound with protein.
I have created ACE and NME group in the molecule to mimic the peptide
environment.
I have optimised molecule with -1 charge and when i delete the ACE and NME
groups the charge of the system was -0.7812.
I am getting confused if i can use the same charges of the atoms to create
force field parameters or some how try to balance the residual -0.2188
charges by manually distributing to certain atoms.
Can you give me suggestions to deal with such systems?
Best Regards
Aashish
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Received on Mon Dec 02 2019 - 00:00:02 PST
