VMD-L Mailing List

From: THANH NGUYEN (ncthanh1986_at_gmail.com)
Date: Thu Mar 31 2011 - 17:46:44 CDT

Thank you all for your suggestions.

I have succeeded in generating a PSF file for NAMD simulation with
associated parameter file. I mainly tried VEGA ZZ, similar with VMD with
more friendly interface.

I will try other suggestions.

Thanks for all.

On Thu, Mar 31, 2011 at 12:59 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> 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):
> http://www.ks.uiuc.edu/Training/Tutorials/
>
> and by reading the psfgen manual here:
> http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> 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 http://www.chemexper.com/chemicals/supplier/cas/919-30-2.html,
> 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
>
>
>
>
> --
> 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
> 

-- 
Thanh Nguyen.
It doesn't matter whether you are a lion or a gazelle.
When the sun comes up, you better start running