[AMBER] Non-integer/zero charges from RESP fitting?

From: Kenneth Huang <kennethneltharion.gmail.com>
Date: Tue, 12 Jan 2021 14:18:04 -0500

Hi all,

I've noticed some odd behavior when I'm trying to fit the charges using the
RESP procedure for several modified nucleic acids, but I'm not sure if it's
just a rounding error.

The setup I have is to feed in the ESPs for the from Gaussian in the same
flow Cornell et al did (ie, DMP, DGN, DAN, DCN, DTN, modified NAs) and
restrain the charges on the sugar except C1'/H1', O5/3', H5/3', for the
nucleosides with the overall charge set to 0, ie

> inosine
> 0 30
> 1 0
> 8 0
> ...
> 1 -1
> 8 0
> 1 0

With restraints to make the O5'/H5' of the nucleosides and the CH3 on the
DMP to add up to zero so I can 'remove' them for the full nucleotide.

The odd thing I've noticed is that while the canonical nucleosides
themselves add up to zero, my modified NAs are all very slightly off
(0.000001). My instinct is that it's a rounding error, but when I check the
output, it says the net charge should be 0,

> Reading input for molecule 6 weight: 1.000
> inosine
> Total charge (ich): 0
> Number of centers: 30

So I tried to dig around in the RESP code and I think the section
responsible for it is

> c as long as ncharge is not -99, implement the "total charge" constraint
> c
> if( ncharge .gt. -99 ) then
> nlgrng= nlgrng + 1
> c
> if( nlgrng .gt. maxlgr) then
> write(6,'(t2,a,i3,/,t2,a,i3)')
> . ' Too many charge-group constraints', nlgrng,
> . ' Maximum allowed: ', maxlgr
> stop
> endif
> grpchg(nlgrng)= float( ncharge)
> do j= ifirst, ilast
> lgrcnt(nlgrng,j)= 1
> enddo
> endif
> return
> end

Which from my limited understanding of it, looks like it should restrict
the charge to N decimal places (6?) which leaves me puzzled as why it'd be
unable to zero the charges, instead of leaving them at 0.000001? Or am I
missing something very obvious?



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Received on Tue Jan 12 2021 - 11:30:01 PST
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