VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Thu Feb 15 2007 - 08:16:06 CST

Hi Peter,

I forgot to mention this detail. I'm indeed specifying the topology
file I want to use. I wasn't very clear, though, because in order to
build the psf file, I need to use 3 different topology files. Anyway,
I merged the topologies in one file and will run it again. I'll let
you know if it didn't go well.

Thanks!
Michel

2007/2/15, Peter Freddolino <petefred_at_ks.uiuc.edu>:
> Hi Michel,
> out of curiosity, why do you have the -top switch in there? If you
> specify -top, autopsf replaces the default topology file with whatever
> file(s) you list after that switch. If you run
> autopsf -mol 0
> or specify a topology file after -top, it should work.
> Peter
>
> L. Michel Espinoza-Fonseca wrote:
> > Hi all,
> >
> > I'm trying to create psf & pdb files for a molecule using the autopsf
> > (I don't have any other option, the whole molecule is formed by at
> > least 300 segments). I'm using the command line to achieve it. When I
> > type the following:
> >
> > autopsf -mol 0 -top
> >
> > I get this:
> >
> > Info: generating structure...
> > unknown patch type NTER
> > ERROR: failed on end of segment
> > MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> >
> > And the program crashes.Then I tried to do this (after "resetpsf"):
> >
> > autopsf -mol 0 -top -noterm
> >
> > and I get exactly the same error. I'm using VMD 1.8.5 under Fedora
> > core 4. Do you have any ideas on how to solve this problem?
> >
> > Thanks!
> > Michel
>