AMBER Archive (2006)

Subject: Re: AMBER: question about solvatecap commander

From: mfyang (mfyang_at_gmail.com)
Date: Tue Mar 07 2006 - 21:07:08 CST

Hi, aini,

Can you provide your input file for your MD run?
I guess you assigned a wrong value to ntb.

Mingfeng

On Tue, Mar 07, 2006 at 09:46:41PM -0500, aini_at_umdnj.edu wrote:
> Dear Amber users,
>
> I am trying to perform a MD simulation on the extracellular loop region of
> a transmembrane protein. I used solvatecap to add water around this region.
> Then I want to minimize the protein first. And sander is just hanging and
> didn't proceed.
> I checked the .out file. See below
> | Flags:
>
> getting new box info from bottom of inpcrd
> | peek_ewald_inpcrd: Box info not found in inpcrd
> |Largest sphere to fit in unit cell has radius = NaN
>
> The program seems to stop here. Does anyone know what might be the problem?
> And what will be the best way if I just want to simulate the loop region
> without altering the other part of the protein?
> Thanks a lot! Any help would be appreciated.
>
> aini
>
> --
>
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