VMD-L Mailing List

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Nov 22 2005 - 18:12:31 CST

That's good. And yes, both files with extensions *.rtf and *.inp contain the same information. The thing here is that CHARMM (the program) is able to read these files, and also the *.str ones. I suggest you to open them and explore them, you'll see that they contain the same information :)
 
Cheers,
Michel

________________________________

From: Ana Celia Araujo Vila Verde [mailto:avilaverde_at_engr.psu.edu]
Sent: Tue 11/22/2005 5:49 PM
To: Michel Espinoza-Fonseca
Subject: RE: vmd-l: psfgen error: MOLECULE DESTROYED BY FATAL ERROR

Thank you Michel,

It works now.

What threw me off is that at Alex M. webpage, from where I got the files in the first place, I didn't find a file called top_all27_prot_lipid.inp, but one called top_all27_prot_lipid.rtf (different extension) and I didn't know if the *.rtf file that I found was the same as the *.inp file mentioned in the tutorial. They seem to be the same (if anyone knows for sure that they are not, please let me know).

Thank you,

Ana

_________________________________
Ana Célia Araújo Vila Verde
Penn State University
Department of Chemical Engineering
Fenske Laboratory
University Park, PA 16802
USA

Phone: +(1) (814) 863-2879
Fax: +(1) (814) 865-7846
avilaverde_at_engr.psu.edu
_________________________________

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Michel Espinoza-Fonseca
Sent: Tuesday, November 22, 2005 5:48 PM
To: Sergio Anis; vmd-l_at_ks.uiuc.edu
Subject: RE: vmd-l: psfgen error: MOLECULE DESTROYED BY FATAL ERROR

I don't think that it's a problem with CMAP (psfgen does not recognize it: it just skips it!). I guess that the problem is that your input file is not complete... You should have something like this:

topology toppar/top_all27_prot_na.inp
alias atom ILE CD1 CD
alias atom GLY OXT OT1
alias residue HIS HSD
segment U { pdb ubqp.pdb
}
coordpdb upqp.pdb U
guesscoord
writepdb U-apo.pdb
writepsf U-apo.psf

Then the program shouldn't complain.
You can get the parameter files from Alex M. webpage:

http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm

Espero que funcione,
Cheers,
Michel

________________________________

From: owner-vmd-l_at_ks.uiuc.edu on behalf of Sergio Anis
Sent: Tue 11/22/2005 3:58 PM
To: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: psfgen error: MOLECULE DESTROYED BY FATAL ERROR

it's a version incompatibility problem, you can either delete all the CMAP references in the topology file or, the best option is to look for the topology file included in the tutorial's files

cheers
sergio

Ana Celia Araujo Vila Verde wrote:
> Hi,
>
>
>
> I'm a new user of VMD. I'm trying to follow the NAMD tutorial to learn
> how to generate a psf file.
>
>
>
> I'm running VMD on a Window XP machine, but NAMD is not installed there.
>
>
>
> Here's what I did:
>
> I did not use the files provided for tutorials available at UIUC
> website. Instead, I went to the Protein Databank to get the pdb file for
> ubiquitin.
>
>
>
> I opened in VMD, and typed
>
> *set ubq [atomselect top protein]*
>
> *$ubq writepdb ubqp.pdb*
>
> * *
>
> on the TkConsole.
>
>
>
> I know the tutorial at this point tells me to close the console and to
> use the Unix terminal to type in the remaining commands, but if I try to
> do it in my DOS window it doesn't work (doesn't even know what package
> means). So, I keep the TkConsole open and continue typing commands in it:
>
> *package require psfgen*
>
> *topology top_all22_prot.inp* (I know it's not the one the tutorial
> recommends but I couldn't find that one in the CHARMM website. The
> closest I could find would be top_all27_prot_lipid.rtf but this led to
> the error message "ERROR! FAILED TO RECOGNIZE CMAP").
>
>
>
> *alias residue HIS HSE*
>
> *alias atom ILE CD1 CD*
>
> *segment U {pdb ubqp.pdb}*
>
> * *
>
> The feedback to this instruction is:
>
> /building segment U/
>
> /ERROR: Unable to open pdb file ubqp.pdb to read residues/
>
> / /
>
> /MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over./
>
> /ERROR: failed while building segment/
>
>
>
> I'd really appreciate some help here as I have no idea what I'm doing wrong.
>
>
>
> Thanks in advance,
>
>
>
> Ana
>
> _________________________________
>
> Ana Célia Araújo Vila Verde
>
> Penn State University
>
> Department of Chemical Engineering
>
> Fenske Laboratory
> University Park, PA 16802
>
> USA
>
>
>
> Phone: +(1) (814) 863-2879
> Fax: +(1) (814) 865-7846
>
> avilaverde_at_engr.psu.edu
>
> _________________________________
>
>
>