Re: Homologous structure as stating flexible fitting model

From: Miro Astore (
Date: Wed Nov 06 2019 - 21:09:12 CST

Hi Yan,

I'm not sure how you would do this specifically because I don't have
experience with MDFF which it sounds like you will need.

I think a good plan might be to follow this tutorial and when you get to
this step in the .namd configuration file this step generates write a
collective variables module file to keep the RMSD between the homologous
structure and your target protein from deviating.

Best, Miro

On Thu, Nov 7, 2019 at 1:39 PM Zhang Yan <> wrote:

> Hi Miro,
> What I want to do is flexible fitting a high-resolution structure to a low
> resolution cryo-electon microscopy density map. And the high resolution
> structure is a homologous model downloaded from PDB data bank. Which
> collective variable I need to use?
> Thank you very much!
> Yan
> 在 2019年11月6日,下午3:27,Miro Astore <> 写道:
> Hi,
> What are you trying to do exactly? Are you trying to constrain a different
> one protein to keep the same tertiary structure as your homologous model?
> If so you should be able to use a collective variable. If you're trying to
> use MDFF, I don't have experience here sorry but I'm sure someone will.
> As regards to your sequence question. You will not need to change the
> sequence, you will have to choose which section of the longer protein
> corresponds with the shorter one and then you simply NAMD to use the CAs as
> your reference for your collective variable.
> We'll need a bit more detail though.
> Best, Miro
> On Wed, Nov 6, 2019 at 6:12 PM Zhang Yan <> wrote:
>> Hi all,
>> I want to perform flexible fitting using NAMD2, but my starting model is
>> a homologous structure, which the sequence is not the same as my sample. Is
>> it necessary to change the sequence to mine? If so, how can I change the
>> homologous structure’s sequence to mine sequence?
>> Their length is different, I don’t how to change it to be the same. Any
>> suggestions or help are appreciated.
>> Best
>> 张艳
>> Yan Zhang,
>> Associate Professor,
>> Institute of Biophysics,
>> Chinese Academy of Sciences
> 张艳
> Yan Zhang,
> Associate Professor,
> Institute of Biophysics,
> Chinese Academy of Sciences

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