Hi Manuel,
Can you post the Gaussian command flags that you're using? If these truly
are Cu(II), the presence of such open-shell systems makes properly
simulating them more difficult and time-consuming.
Eric Berquist
Lambrecht Lab
University of Pittsburgh
On Thu, Jul 4, 2013 at 12:57 AM, <mmaestre.gate.sinica.edu.tw> wrote:
> Dear Amber community members,
>
> I wrote a week ago about some trouble with organizing my files for
> parametrization of a laccase metal cluster using MCPB. Luckily, I've
> managed to iron those out, and now I am at the stage of the "small model"
> as described in the MCPB tutorial. Sadly, the gaussian optimization is
> doing pretty crazy things.
> So, first of all, the laccase metal cluster is a tetranuclear copper
> center, where all coppers (at least in the state I am working with) should
> be CuII. Three of the coppers form a trinuclear center, while the fourth
> one is some 13A away, and is by itself. The trinuclear center is complexed
> by six histidines and two hydroxide ions, while the mononuclear one is
> complexed by two histidines and one cysteine.
> Up until now, I have tried two strategies:
> a) optimize both clusters together (after all, they should interact with
> each other during protein activity).
> b) Optimize each cluster by itself.
>
> In case a) convergence is very slow (it actually has not happened yet,
> after one week), but the worrying bit is that the two clusters separate in
> space. I don't think that is what they should do, is it?
> In case b) the mononuclear cluster optimizes within a couple of hours, and
> looks very good, but the trinuclear one fails after ~2-3 days, with the
> following error message:
> Berny optimization.
> Using GEDIIS/GDIIS optimizer.
> Bend failed for angle 64 - 123 - 120
> Tors failed for dihedral 58 - 64 - 123 - 120
> Tors failed for dihedral 67 - 120 - 123 - 64
> Tors failed for dihedral 121 - 120 - 123 - 64
> Tors failed for dihedral 122 - 120 - 123 - 64
> FormBX had a problem.
> Error termination via Lnk1e in /pkg/chem/gaussian/g09d01/g09/l103.exe at
> Wed Jul 3 06:27:09 2013.
> Job cpu time: 31 days 16 hours 57 minutes 44.0 seconds.
> File lengths (MBytes): RWF= 1314 Int= 0 D2E= 0 Chk= 108
> Scr= 1
> Error: segmentation violation
> rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff
> rdx 0000000000006a2e, rsp 00007fff96d640c8, rbp 00007fff96d646b0
> rsi 000000000000000b, rdi 0000000000006a2e, r8 0000000000000000
> r9 00002ab5d28a6e10, r10 ffffffffffffffff, r11 0000000000000202
> r12 0000000000000000, r13 0000000000000000, r14 00007fff96d646f8
> r15 00000000000003e6
> --- traceback not available
>
> Which, I suppose, means that some of the bonds are in a very awkward
> position.
> I am really quite a newbee on this whole metalo-cluster modeling thing, so
> it would be absolutely great if someone could give me a hand!
> Thank you very much in advance!
> Manuel Maestre Reyna
>
> Academia Sinica
> Institute of Biological Chemistry
> 128, Academia Road Sec. 2, Nankang, Taipei 115, Taiwan
>
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Received on Fri Jul 05 2013 - 17:30:02 PDT
