VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Sep 15 2015 - 09:48:02 CDT

Wouldn't it be autopsf -top [list top1.str top2.str top3.str] ? Running
foreach on a string input won't get the results you expect, as it will
chop it up one character at a time in my experience. That *should* work
for what you describe. How many disulfides do you have though? Usually I
don't find it to be a big deal for my projects (maybe 1 or 2), and I
just put them in manually with a patch statement.

-Josh

On 09/15/2015 08:53 AM, Kevin C Chan wrote:
> Dear Users,
>
> I am struggling with the autopsf plugin.
>
> Sometimes we are in need of feeding some user-defined topologies into
> Autopsf. I often work with the command-line interface and the -top
> command bothered me. I have read through the tcl code and I fed
> topologies separated by "space"
>
> autopsf -top "top1.str top2.str top3.str"
>
> But it still gives me things like
>
> psfgen) building segment O1
> psfgen) reading residues from pdb file
> system_psfgen_autopsf-temp.pdb_O1.pdb
> psfgen) unknown residue type DOPC
>
> And of course residue DOPC has been well defined in top1/2/3.str.
>
>
>
> In addition to solving -top problem of autopsf, here is my very
> original intention:
>
> I have a rather complicated system: a protein consists of S-S bond and
> membrane composed of some lipids with self-defined topology.
>
> I have three problems for different approaches on smoothly generating
> a psf for the system:
> 1. My autopsf could not read too many topology files (described above)
> 2. I could write psfgen tcl codes for the membrane but I found it very
> difficult to integrate the automatic S-S bond detection part into a
> simple psfgen code
> 3. GUI version of autopsf is rather buggy, I feed the topology files
> and it crashes when reading.
> 4. I would like to try autopsf reading one single topology file
> instead of multiple but I do not know how to correctly combine them. I
> am using CHARMM36ff and I would like to combine rtf and some str files.
>
>
>
> Thanks in advance for any experience sharing. Reply to any of the
> above question would be very helpful.
>
> Regards,
> Kevin