VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 04 2003 - 15:29:38 CST

Dear Yongmei,
  Ah, yes, this is the problem. Please download the final released
version of VMD 1.8, and you should be in good shape. I strongly
recommend anyone running beta versions to upgrade to the released
version!!!! :-)

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 04, 2003 at 04:23:27PM -0500, Yongmei Wang wrote:
> Dear John:
>
> I am using VMD1.8a21, in the molecule file browser, it only has parm option,
> it does not have parm7 type.
>
> Maybe I am not using the correct version of VMD?
>
> Yongmei
>
> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: Tuesday, February 04, 2003 4:01 PM
> To: Yongmei Wang
> Cc: vmd
> Subject: Re: VMD 1.8 problems with AMBER parm and crd file
>
>
>
> Dear Yongmei,
> When you load your Parm file, can you double-check that its loading
> using the type "parm7" in the file type listing in the molecule file
> browser form? If this is the case, I'll need to see the file you're
> loading in order to determine what problem you might be running into.
> If you encounter any error like that with the parm file, then the
> trajectory file will fail to load as well (best case).
>
> Let me know about the file type. If you are in fact loading with
> the filetype as "parm7" then I'll need a copy of the parm file that
> causes the problem.
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Feb 04, 2003 at 03:57:18PM -0500, Yongmei Wang wrote:
> >
> > Hi, I am new on this email listing.
> >
> > I am using VMD 1.8 on SGI/IRIX6.5 and amber7.0. Somehow I can not load
> parm
> > and coordinate files created using leap under amber7.0.
> > it complains " unexpected EOF file in the parm file". The parm file is
> fine,
> > I used it to run the sander. What's the problem?
> >
> > THen I tried to load the parm file and the trajectory file mdcrd created
> by
> > sander, this time it complains "memory allocation error", not enough swap
> > space.
> >
> > Anyone has any idea what's the problem?
> >
> > Thanks
> > Yongmei
> >
> >
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078