Hi Dave,
On 14/8/2010, at 9:20 a.m., case wrote:
> On Fri, Aug 13, 2010, Ben Roberts wrote:
>
>>>> The first is that both sleap and tleap seem to create spurious bonds
>>>> between the two nickel ions, which are far enough apart (3.5 to 4 Ã )
>>>> that they shouldn't be bonded to each other.
>
> The problem is in the way the metal ion library files are created. The
> distance between the atoms is irrelevant.
>
>> loadamberprep 1FWJ_chg2.prep
>
> This creates a residue with "head" and "tail" atoms, so it will create bonds
> to neighboring residues unless that is turned off with TER cards.
>
> Note that the standard ions Amber uses have null heads and tails, which
> explains why you were not getting bonds between Na+ ions, even though your
> PDB file treats Na+ and NI1 in equivalent ways.
>
> To see this, type the following commands in tleap
>
> loadoff ions08.lib
> desc Na+
> loadamberprep 1FWJ_chg2.prep
> desc NI1
>
> You will see the difference.
Got it. Thanks for the advice.
> So, Martin's scripts (or whatever you are using) either should create ions
> in a way analgous to how Amber handles ions (see
> amber11/dat/leap/lib/ions08.cmd), or arrange for TER cards to be put into the
> pdb files.
I'll make sure that's known.
> Since only two lines of the pdb file were relevant, you could have
> experimented to find a small example that still illustrated the problem.
> (See, e.g., below).
True. I'll start doing that in future.
Thanks again.
Ben
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Received on Mon Aug 16 2010 - 15:30:03 PDT
