VMD-L Mailing List

From: Walter Rocchia (Walter.Rocchia_at_iit.it)
Date: Mon Feb 18 2013 - 12:21:12 CST

Hi,
the problems you encountered are due to the high symmetry (atom
co-planarity in this case) of the C6H6 system.
In order to be compliant with these highly symmetric systems,(for
instance, the fullerene buckyball is another example of a tricky one), we
realized the NanoShaper tool
http://www.electrostaticszone.eu/index.php/research/11-research/3-ms

It has his own visualizer but can also be interfaced with VMD, with a bit
of effort.

Similarly to MSMS, it takes a .xyzr input file. Its output, in .off
format, can be converted in .face and .vert files using the off2msms.py
script, which can be then fed to VMD.
A precompiled version of NanoShaper 0.3.1 is available for Windows
operating system, while source code and installer are available for most
Linux distributions.
 
Yours
Walter
*********************************************************************

Walter Rocchia, PhD
Team Leader - Computational Chemistry
Drug Discovery and Development
ISTITUTO ITALIANO DI TECNOLOGIA
Via Morego 30, 16163 - Genova, Italy
Phone: +39 010 71781552 Room: 1/31
Fax: +39 010 7170187
 

Il giorno 18/2/2011 4:54 PM, "John Stone" <johns_at_ks.uiuc.edu> ha scritto:

>
>Hi,
> There are a number of cases where Surf doesn't work as well as it
>could. Have you tried using MSMS or QuickSurf instead? MSMS should
>produce a surface of at least as good quality as that produced by
>Surf, but it may likely work in cases where Surf is doing poorly.
>
>If you don't have to see the solvent accessible surface, then QuickSurf
>is much faster than both Surf or MSMS, and it handles many cases that
>neither Surf or MSMS can handle.
>
>To use MSMS, you will need to download it from Scripps:
> http://mgltools.scripps.edu/downloads
>
>Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>On Mon, Feb 18, 2013 at 04:45:38PM +0100, Sabine Reisser wrote:
>> Hi everyone,
>>
>> I parametrized and geometry-optimized a single benzol C6H6 Ring, saved
>> it in a pdb-file and tried to visualize its surface within VMD (Drawing
>> method -> Surf). In all of my tries, the surface never completely
>> closed. I noticed that the amount of closing depends on the
>>coordinates.
>> In the beginning, I had all z coordinates on 0 since the molecule is
>> planar. For this, I good the worst results, the surface contained many
>> individual patches which didn't fuse. Translating and rotating the
>> coordinates enhanced the result. It also seemed that negative
>> coordinates are deprecated by the SURF module. I also tried pqr
>> structures with different radii, which changed the surface volume as
>> expected but didn't enhance closing.
>>
>> I suppose that there is a bug or at least some incompleteness in the
>> SURF code. If somebody could provide a fix or a workaround, I would be
>> very glad.
>>
>> Thanks for reading and
>> Cheers,
>>
>> Sabine
>
>--
>NIH Center for Macromolecular Modeling and Bioinformatics
>Beckman Institute for Advanced Science and Technology
>University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078