VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Feb 15 2007 - 08:11:49 CST

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