Date: Mon Mar 28 2011 - 19:11:42 CDT

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

  • application/octet-stream attachment: APTES.mol