VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Oct 25 2005 - 22:34:13 CDT

Here: http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial.pdf

Yep, you use psfgen to make it, then add the bonds with your text
editor of choice.

On Oct 25, 2005, at 8:05 PM, Craig Maloney wrote:

> Hi.
>
> Which NAMD tutorial? Where can I find it?
>
> Just to make sure: I'd like to generate a more or less "blank" psf
> file (from my pdb file) and then add bonds to that file myself. Is
> this the kind of thing that "psfgen" (which I read about in the NAMD
> manual) will allow me to do?
>
> Thanks.
>
> --Craig
>
> On Oct 25, 2005, at 5:32 PM, JC Gumbart wrote:
>
>> It's pretty easy to add bonds actually to the psf file directly. See
>> the appendix of the NAMD tutorial for specifics on how the file is
>> laid out. Basically, you will have to adjust the numbers of bonds
>> (noted at the beginning of the bond section) and then add the two
>> atoms you want bonded. The bond length and force constant will take
>> the form of that for those specific atoms (defined in the parameter
>> file).
>>
>> To make the psf file in the first place, also see the NAMD tutorial,
>> I believe, for a description of this.
>>
>> On Oct 25, 2005, at 7:16 PM, Craig Maloney wrote:
>>
>>
>>> Hi all.
>>>
>>> I'm currently using LAMMPS to do some MD simulations (not biological
>>> stuff per se). I'd like to manually tell VMD about bonds. I gather
>>> from traffic on this group that I cannot simply add "CONECT" lines
>>> to the pdb files, right? So my question is whether this can be done
>>> from the tcl or python interpreter? Or is there some documentation
>>> somewhere for what these "PSF" files are all about? Or what is the
>>> ETA for implementation in VMD of the CONECT lines feature?
>>>
>>> Thanks much,
>>> Craig
>>>
>>
>>