VMD-L Mailing List

From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Tue Sep 08 2015 - 23:18:47 CDT

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 *