VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Wed Sep 09 2015 - 10:37:09 CDT

To answer your question about MDFF, if you ran the simulation without any
secondary structure restraints or with secondary structure restraints
generated from a bad initial model, it is very likely that the resulting
model will have bad secondary structure (especially if running the
simulation in vacuum). As for why stride is crashing, it is possible your
structure is too large and is causing stride to choke.

On Wed, Sep 9, 2015 at 12:41 AM Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk>
wrote:

> Dear Users,
>
> Sorry for digging this old thread. But I have not yet found the solution
> for this. Maybe let me explain my question again in case this email cannot
> go into the right thread:
>
> I have a quite large protein (a protein lattice in fact) and it is from
> rigid-body docking repeating units into a density map. The docking was very
> crude and we are going to do MDFF on it. However during the preparation of
> psf files, I found VMD fails to generate a New Cartoon representation for
> it which requires guessing secondary structures of it (so of course
> coloring by sec struc also fails).
>
> Then I narrowed down the problem to those single units of protein and
> found all of them are okay to be generated such representation
> individually.
>
> I have examined the proteins and there are some very closely placed atoms
> that might lead to difficult or wrong guesses.
>
> Interestingly, when I thought it is due to bad initial structure and
> continued with my MDFF and obtained a much better structure, the final
> structure with no obvious bad atom positions still fails to generate the
> secondary structure representation. Why?
>
> Another question is, when I have successfully generate a psf file from the
> structure in which atoms are segmented into different segments, wouldn't
> they affect each other's secondary struc guessing even if the atoms are
> placed badly, or would they?
>
>
>
> In addition, here is the error messages from VMD console:
>
> ERROR) Unable to find Stride output file:
> C:\Users\CCHAN2~1\AppData\Local\Temp\3
>
> ERROR) Stride::read_stride_record: unable to read output file from Stride
> ERROR) Call to Stride program failed.
>
> And it gives me a pop-out window saying stride_WIN32.exe has stopped
> working.
>
>
> Thanks in advance,
> Kevin
>
> The pop-up window indicating the STRIDE stopped means that it crashed
>> for some reason, and this is why VMD isn't getting output from it.
>> I don't have a particular suggestion for you at this moment, but it might
>>
>> be useful for me to know more details about your structure such as how
>> large
>> it is, etc.
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>> <vmd_at_ks.uiuc.edu?Subject=Re:%20%20Problem%20with%20assignation%20of%20secondary%20structure%20in%20VMD>
>>
>> On Fri, May 08, 2015 at 11:50:35AM +0800, Kevin C Chan wrote:
>>
>> *> Thanks for the reply. *
>> *> *
>> *> It says: *
>> *> ERROR) Unable to find Stride output file: *
>> *> C:\Users\CCHAN2~1\AppData\Local\Temp\3 *
>> *> *
>> *> ERROR) Stride::read_stride_record: unable to read output file from
>> Stride *
>> *> ERROR) Call to Stride program failed. *
>> *> *
>> *> And it gives me a pop-out window saying stride_WIN32.exe has stopped *
>> *> working. *
>> *> *
>> *> Regards, **> Kevin *
>
>