VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Feb 15 2007 - 08:20:20 CST

Hi Michel,
at least in VMD 1.8.6, you'll be able to specify a space delimited list
of of top files after that switch, eg
autopsf -mol 0 -top "file1.top file2.top file3.top"
I forget when I added that though; it may not be in 1.8.5.
Peter

L. Michel Espinoza-Fonseca wrote:
> 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
>>