VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Apr 01 2011 - 02:15:51 CDT

Well I wouldn't say that VEGA ZZ's user interface is more friendly. It
depends on personal taste (and on one's TCL skills:)

Regards,
Ajasja

On Fri, Apr 1, 2011 at 00:46, THANH NGUYEN <ncthanh1986_at_gmail.com> wrote:

> 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
>