VMD-L Mailing List

From: jrhau lung (jrhaulung_at_gmail.com)
Date: Fri Sep 30 2016 - 17:32:37 CDT

Got it, Thanks Ryan.

Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu> 於 2016年10月1日 星期六寫道：

> You can always save the structure at any time from the "File" menu by
> using "Save Coordinates..." or by making an atom selection and using the
> writepdb command. Also, if you are using the chirality plugin and running
> namd after each correction, you should already have the new pdb in whatever
> directory namd is being run.
>
> On Fri, Sep 30, 2016 at 2:36 AM jrhau lung <jrhaulung_at_gmail.com
> <javascript:_e(%7B%7D,'cvml','jrhaulung_at_gmail.com');>> wrote:
>
>> Dear VMD-I friends:
>> Probably due to the homology based structure modeling, the outcome
>> protein structure contains many amino acids do not pass the VMD chirality
>> checkup and need to be manually correct them one by one. Is there a way to
>> update the psf and pdb file after several correction steps? Since a crash
>> in the MD structure optimization after chirality correction will make the
>> structure repairment work to be started all over again. Thanks!
>>
>> sincerly,
>>
>> Jrhau
>>
>