Re: Harmonic restrains

From: Miro Astore (miro.astore_at_gmail.com)
Date: Sat Nov 09 2019 - 03:17:41 CST

Make sure you are using the right options outlined here

https://www.ks.uiuc.edu/Research/namd/2.9/ug/node27.html

Or in colvars https://www.ks.uiuc.edu/Research/namd/2.9/ug/node55.html

On Sat., 9 Nov. 2019, 19:22 Zhang Yan, <yanzhang_at_moon.ibp.ac.cn> wrote:

> Hi,
> How can I run namd with harmonic restraints? I saw from the manual that
> harmonic restrains needs the PDB file containing constraint reference
> positions, but how can I get this PDB file with constraint reference
> positions?
> Many thanks!
> Yan
>
> 在 2019年11月7日,上午11:24,Zhang Yan <yanzhang_at_moon.ibp.ac.cn> 写道:
>
> Hi all,
> I’m trying to do flexible fitting the crystallography structure to a
> cryo-electron microscopy density map. I get some errors which I attached in
> the attachment. I’m not sure which parameter is needed to be changed to
> avoid these errors. Any suggestions or help are appreciated.
> Best!
> 张艳
> Yan Zhang,
> Associate Professor,
> Institute of Biophysics,
> Chinese Academy of Sciences
>
>
> <屏幕快照 2019-11-07 上午10.10.09.png>
>
>
> 张艳
> Yan Zhang,
> Associate Professor,
> Institute of Biophysics,
> Chinese Academy of Sciences
>
>
>
>
>

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