Dear all,
We are simulating a DNA duplex with a few modified DNA bases. We plan to
use OL15 force field. We are preparing the modified DNA base parameters by
the following method:
1. Optimizing and calculating esp charges using gaussian
2. RESP fitting using antechamber
3. Using parmchk2 to generate the frcmod files.
We have the following queries in this:
1. The first is regarding the atom type to be used in this case in
antechamber. For small organic molecules, we have used gaff or gaff2. But
since this is a DNA base, we wanted to know if we should use the AMBER
types. Could someone please suggest any guidelines regarding this?
2. When we used AMBER atom types, we got multiple "ATTN needs revision"
messages in the frcmod. We tried to fix this manually. For instance, one
such error happened in the C-CM-F angle. We copied C-CC-F from the gaff.dat
and placed the values manually in the frcmod. Is this procedure acceptable?
Because initially, we are using amber atom type and then borrowing some
parameters from gaff. Though we have seen some posts related to this, a
systematic overview was not found. Kindly advise in this regard.
Thank you all in advance
Regards,
Sruthi Sudhakar
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Received on Tue Sep 05 2023 - 05:00:02 PDT
