Dear all,
I am presently working through this tutorial
(
https://ambermd.org/tutorials/basic/tutorial5/), attempting to apply
RESP charges. As part of this process, I've introduced additional charge
constraints in the ANTECHAMBER_RESP1/2.IN files. These constraints
relate to the peptide bond atoms and are set to match the FF charges,
also stipulating that the partial charge of all four atoms must equate
to zero. The structure encompasses two peptide bonds.
Here is the appended section to the ANTECHAMBER_RESP1.IN:
1 -0.56790
1 34
1 0.59730
1 32
1 -0.41750
1 48
1 0.27190
1 49
4 0
1 34 1 32 1 48 1 49
# next peptide bond
1 -0.56790
1 30
1 0.59730
1 20
1 -0.41570
1 26
1 0.27190
1 36
4 0
1 30 1 20 1 26 1 36
I'm encountering an issue when running resp; the charges in the qout
file are all returned as NaN. Interestingly, when I include constraints
for only one peptide bond, resp generates a qout file with charges. This
holds true for both peptide bonds when individually included. For your
convenience, I've attached the structure.xyz and resp input and output
files. At this stage, I'm unsure how to move forward and I'm seeking any
insights or advice you could offer. Any assistance will be greatly
appreciated.
Thank you in advance for your time and help.
Best regards,
Albert
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 07 2023 - 01:30:02 PDT
