AMBER Archive (2004)

Subject: Re: AMBER: Close contact warnings

From: David A. Case (case_at_scripps.edu)
Date: Tue Feb 17 2004 - 10:39:22 CST

On Tue, Feb 17, 2004, L Jin wrote:
>
> After I load amber prep file into xleap, I used check unit and was given the
> following message:
>
> Unit Editor: Warning: Close contact of 0.323280 angstroms between .R<4SN
> 1>.A<ON3 25> and .R<4SN 1>.A<H51 29>

...etc

>
> I know they are just some warnings and I can save my prmtop and inpcrd files
> without problems. But I suspect the Close Contact warnings are the reason
> which make the subsequent minimizaion clash with the following abnormal
> errors:
>
> Frac coord min, max: -116.333726 117.209705
> The system has extended beyond
> the extent of the virtual box.

It is certainly true that such very bad contacts could cause minimizations
to fail in this way, but it is unusual. How many steps have you run before
you get the above failure?

>
> I have run some short minimizaiton and got the output files every step. And
> I found that the problems seem to be the VDWAALS = 26975175.0840 EEL =
> -356.7031.

This initial vdW energy should not cause the kinds of problems you state.
What happnes to these energies during the course of the "short minimizations"?
Run just steepest descent (ntmin=2) if you have not been doing that. I would
think that after 50 steps of minimization, you should have acceptable
energies. But you may have such a bad initial structure (what does it look
like visually) that Amber is unable to correct it. In that case, you will
have to fix the starting coords.

..good luck...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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