From: John Stone (
Date: Thu Mar 31 2011 - 14:59:37 CDT

  There isn't an MDL mol file plugin distributed with VMD presently, but
you can use OpenBabel or similar tools to convert the file. In terms of
generating a PSF, unless the structures use standard PDB atom naming
conventions you will likely not be able to use AutoPSF to automatically
generate a matching PSF file since it won't know which CHARMM parameters
to assign etc. You would most likely have to assign parameters etc yourself
using psfgen text commands. This isn't my area of expertise, but my
best suggestion is to familiarize yourself with these issues by working
through the tutorials on parameter and topology files here (scroll down):

and by reading the psfgen manual here:

  John Stone

On Tue, Mar 29, 2011 at 11:11:42AM +1100, THANH NGUYEN wrote:
> Hi everyone.
> I'm new to VMD, so any suggestion would be greatly appreciated.
> I downloaded the molfile (.MOL) for APTES (3-AMINOPROPYLTRIETHOXYSILANE)
> from, this
> file can be viewed by Jmol (another viewer for chemical structure) BUT NOT
> VMD. (APTES.mol attached, it's a small molecule compared with proteins,
> DNAs... only 48 atoms)
> So I used a conversion tool online named MM.Convert to convert .mol file
> to .pdb file and the pdb file now can be viewed in VMD. (APTES.pdb
> attached)
> However, when I tried to generate a PSF file from APTES.pdb (prior to a
> NAMD simulation) using VMD's AUTOPSF with topology files from VMD
> installation folder (I tried all the topology files), it ends up with
> errors or a funny-looking 2D structure of APTES (of course completely
> wrong)
> I've been struggling with this issue for a while, it might sound easy but
> I don't know how.
> Any suggestion would be appreciated.
> Thank you.
> --
> Thanh Nguyen.
> It doesn't matter whether you are a lion or a gazelle.
> When the sun comes up, you better start running

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