I don't know what's happening (maybe others here do) but it may help to
provide the Amber version, which MD code you tried (sander, pmemd,
pmemd.cuda etc), if you ran in parallel or not, if the test cases all
passed for your installation, if you have any non-standard force field
libraries, if this is the first minimization after building the system, the
input file that you used, and so on.
On Sat, Mar 16, 2024 at 10:54 PM Sasha Buzko via AMBER <amber.ambermd.org>
wrote:
> Hi All,
> I have a relatively large system (70 kDa) solvated using OPC water model.
> When solvation is done with a 10 A margin, everything runs just fine.
> However, when I try to add more solvent and go to 20 A, minimization fails
> with the below message:
> Coordinate resetting cannot be accomplished,
> deviation is too large
> iter_cnt, my_bond_idx, i and j are : 5 2870 5814 5817
>
> The restart file is not written even when I specify ntwr=10 and the
> failure is at step 110. The error message is highly strange as well, since
> it refers to the amide N and carbonyl O atoms of the same residue. Not sure
> how it's possible for them to become too close (or too far), especially
> when the entire protein structure is restrained.
> And finally, the same starting structure behaves perfectly fine when the
> number of waters is lower (and the box is smaller). With the smaller box,
> production MD runs to 200 ns without incident.
>
> Has anyone seen anything like this? Why are extra waters triggering these
> failures? I may well be missing something but this doesn't seem to make
> sense.
>
> Thanks in advance!
>
> Sasha
>
>
> ---
> Oleksandr "Sasha" Buzko
> Computational Biology
> ImmunityBio
> 9922 Jefferson Blvd
> Culver City, CA 90230
>
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Received on Sun Mar 17 2024 - 14:30:02 PDT
