VMD-L Mailing List

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Mon Feb 16 2009 - 17:05:31 CST

Since I have protein inside water, there might be "islands" as you
mentioned.

Thanks again.
Bin

On Feb 16, 2009, at 1:09 PM, John Stone wrote:

>
> Hi,
> Given that it works for one selection but not another, this may
> simply
> be the normal behavior of MSMS where it may or may not generate an
> output
> surface if it gets a set of points it doesn't like. This isn't
> anything
> specific to VMD. You can send MSMS a set of atoms that it will
> refuse to
> generate a surface for in some cases. The complaint from VMD is
> occuring
> because it's not finding the MSMS output file, but from what you're
> saying,
> it sounds to me like MSMS is just not producing one for its own
> reasons.
> I would suggest taking a close look at what is actually selected
> in those two cases and see if you have "islands", voids, or other
> unusual
> clumping in the set of atoms sent to MSMS, those are often the cases
> it
> gets unhappy about.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sun, Feb 15, 2009 at 10:43:00PM -0800, BIN ZHANG wrote:
>> Hi, John:
>>
>> I am using VMD 1.8.6 on Mac Leopard 10.5.
>> MSMS seems not working for selection "water" but works for "water and
>> noh".
>> Any idea?
>>
>> Thanks,
>> Bin
>>
>>
>>
>> On Feb 15, 2009, at 10:27 PM, John Stone wrote:
>>
>>>
>>> Hi,
>>> What version of VMD are you using, and on what platform?
>>> This error could indicate one of several potential issues,
>>> but to start out with I need more information.
>>>
>>> Cheers,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Sun, Feb 15, 2009 at 09:54:52PM -0800, BIN ZHANG wrote:
>>>> Dear all:
>>>>
>>>> I was trying to use the drawing method "MSMS", but got the
>>>> following
>>>> error :
>>>>
>>>> ==============================
>>>> Compilation flags -O3 -DVERBOSE -DTIMING -DFUNCPROTO -
>>>> force_cpusubtype_ALL
>>>> INPUT /tmp/vmdmsms.u501.991 116426 spheres 0 collision only, radii
>>>> 1.000 to 2.270
>>>> PARAM Probe_radius 1.500 density 1.500 hdensity 3.000
>>>> REDUCED SURFACE ...
>>>> RS component 0 identified 10399 15337 31589
>>>> 0 free edge(s) found in component 0
>>>> RS component #faces #edges #free_edges #vertices genus
>>>> 0 24744 37116 0 11468 453
>>>> Time Reduced Surface real: 2.89 user: 2.70 sys: 0.04
>>>> ANALYTICAL SOLVENT EXCLUDED SURFACE...
>>>> Component 0
>>>> Time Surface real: 0.38 user: 0.32 sys: 0.03
>>>> ERROR) Cannot read MSMS facet file: /tmp/vmdmsms.u501.991.face
>>>> Info) Could not compute MSMS surface
>>>> Info) Done with MSMS surface.
>>>> ==============================
>>>>
>>>> Can someone explain to me what's wrong with it?
>>>> I ran the test example came with the binary, and it worked just
>>>> fine.
>>>>
>>>> Thanks,
>>>> Bin
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>> --
>>> NIH Resource for Macromolecular Modeling and Bioinformatics
>>> Beckman Institute for Advanced Science and Technology
>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> -------------------------------------------------------------
>> The tree of liberty must be refreshed from time to time with the
>> blood
>> of patriots and tyrants.
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078

-------------------------------------------------------------
The tree of liberty must be refreshed from time to time with the blood
of patriots and tyrants.