Re: Harmonic restrains

From: Miro Astore (miro.astore_at_gmail.com)
Date: Sat Nov 09 2019 - 19:25:30 CST

https://salilab.org/modeller/

The other thing you can do is build your initial structure with this.

On Sat., 9 Nov. 2019, 20:17 Miro Astore, <miro.astore_at_gmail.com> wrote:

> 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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