Date: Wed, 26 Jul 2023 16:54:59 +0000
Dear Amber Community,
I am trying to run MD simulations with a peptide which has a covalently modified cysteine. I followed the following steps.
1. I generated a mol2 of the modified residue, capped it with ACE and NME and calculated the charges using antechamber.
2. Since, I want to use ff15ipq for the simulations, I replaced the backbone charges and names using amino15ipq_10.0.lib.
3. Then, I generated an off file and modified it to have information about bonding to neighbouring residues.
4. I generated the missing parameters using parchchk2.
I can now build systems using this residue, but it has a net charge of 0.23 as I replaced the charges in step2.
This procedure seems to be followed in many studies in the literature.
How is the charge neutralized in these cases? Should I just distribute the charge equally to all the other atoms, or is there a better way of doing this?
Thanks.
Amin Sagar
Senior Computational Chemist
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BicycleTx Ltd
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