AMBER Archive (2009)

Subject: Re: [AMBER] [Fwd: problem with minimization]

From: moitrayee_at_mbu.iisc.ernet.in
Date: Thu Oct 22 2009 - 13:53:11 CDT

Thanks a lot for the reply. I removed the short contacts and the minimisation
and equillibration showed no error. But the simulation blew up in the very first
step. I have tried varying the solvent box sizes (increase) but then the
minimization itself blows up.
Can you please suggest me what can I do.
I would be really grateful if you can suugest me a way out of this problem
Thanks a lot in advance.

Sincere Regards,
Moitrayee

>> WARNING: There is a bond of 30.500389 angstroms between:
>> ------- .R<RA3 712>.A<N7 16> and .R<RA3 712>.A<C5 17>
>> WARNING: There is a bond of 31.529394 angstroms between:
>> ------- .R<RA3 712>.A<C8 14> and .R<RA3 712>.A<N7 16>
>
> That is worth figuring out.
>
>> WARNING: The unperturbed charge of the unit: -0.999880 is not zero.
>
> It looks like if there are as manya s 153 ions, rounding errors in the
> charge calculation mean you are coming out an ion short. You can add
> this explicitly with another addions cmd for now.
>
> The bond length thing seems the more likely cause of minimization
> failure.
>
> Bill
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber