Re: [AMBER] vlimit exceeded for step

From: David A Case <>
Date: Fri, 9 Mar 2018 21:37:00 -0500

On Sat, Mar 10, 2018, ASMITA SEN wrote:
> My protein system contains an iron(iii) coordination centre at the active
> site with hydroxyl group as one of the ligands. Earlier I have performed
> dynamics with Fe(IV)-oxo system where the dynamics worked fine. I took one
> of the pdbs from trajectories of Fe(IV)-oxo system, added hydrogen to the
> oxygen and prepared Fe(III)-hydroxyl system input files using
> program. The parameters were calculated from QM calculations utilizing
> Gaussian 09 software.

Check the Lennard-Jones parameters of your added hydrogen: does it have
a zero radius. That could certainly cause the symptoms you report.

[I see that I asked this question back on Mar 5: apologies if I missed
your reply.]

> I have tried to check the atom numbers and found that 4822 and 4823
> correspond to the oxygen and hydrogen atoms of OH group that is bound to
> Fe(III) at the active site.

This makes it very likely that the problem lies with the Fe-OH moiety.

One possible approach: if you parameterization process involves gaff,
switch to gaff2. Hydrogens bonded to oxygen have zero vdw radii in
gaff, but not in gaff2. [Ignore if this is not the problem.]


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Received on Fri Mar 09 2018 - 19:00:03 PST
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