Hi all,
Something of a procedural/background question- what is the exact procedure
for determining the charges for modified/unnatural bases at the 5'/3'
termini?
Given the termini are unique, ie their charge is non-integer by design, the
closest I could find is the tutorial here (
https://ambermd.org/tutorials/advanced/tutorial1/section1.htm), but trying
to follow it as close as possible in AmberTools16 with a test run of
something simple of native DG3' nets an EOF runtime error-
resp -O -i dg_resp.in -o dg_resp.out -p dg_resp.pch -t dg_resp.chg -q
> dg-resp1.qin -e dg_esp1.esp
> At line 744 of file resp.F (unit = 5, file = 'dg_resp.in')
> Fortran runtime error: End of file
>
Which I've figured has something to do with how my group constraints are
formatted?
...etc
> 1 0
> 34 -0.6921
> 1 1 1 2 1 3 1 4 1 5 1 6 1 7
> 1 8
> 1 9 1 10 1 11 1 12 1 13 1 14 1 15
> 1 16
> ...etc
>
But I can't see anything that's obviously wrong about it, or did I
misunderstand how the group constraint is meant to work?
Or am I going about this the entirely wrong way? I know in the case of DNA
forcefields, the charges have been relatively fixed since ff94/99- so could
I approach it as an internal base, ie do the ESP/RESP fitting on just the
modified base portion with a methyl cap, and 'stitch' the backbone/sugar
from the source forcefield back together for a complete base?
Best,
Kenneth
--
Ask yourselves, all of you, what power would hell have if those imprisoned
here could not dream of heaven?
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Received on Mon Jul 27 2020 - 00:00:03 PDT
