From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Mar 19 2012 - 02:00:38 CDT
Dear Alisha,
Can you open zero.fep in a file editor? It should look almost identical to
a PDB file. Does it?
Best,
Chris
On Mon, Mar 19, 2012 at 1:56 AM, Alisha "Jonesy" Jones
<jonesan_at_muohio.edu>wrote:
> Hi Chris,
>
> Thanks for the response. I just tried what you suggested and it reads the
> following:
> >Main< (01.ethane-ethane) 14 % mol new setup.psf
> 2
> >Main< (01.ethane-ethane) 15 % mol addfile zero.fep
> Could not determine file type for file 'zero.fep' from its extension.
>
> I also tried: mol new setup.psf zero.psf zero.fep
> and: mol new setup.psf -pdb zero.fep
>
> On the graphical representations interface, setup.psf appears, as well as
> on the VMD Main... it appears as if it is there, but even on changing
> background colors, turning on and off the display, etc., I still fail to
> get my molecule.
>
> Any other advice?
>
> Thanks,
> Alisha
> On Sun, Mar 18, 2012 at 11:40 PM, Chris Harrison <charris5_at_gmail.com>wrote:
>
>> Alisha,
>>
>> What happens if you open the TkConsole, cd to the correct directory, and
>> type:
>>
>> mol new setup.psf
>> mol addfile zero.fep
>>
>> Best,
>> chris
>>
>>
>>
>> On Mon, Mar 19, 2012 at 1:20 AM, Alisha "Jonesy" Jones <
>> jonesan_at_muohio.edu> wrote:
>>
>>> Hello,
>>>
>>> I am working through the FEP tutorial. I am on section 1.1 System
>>> Setup. I am sorry for such an "basic problem" but any help would be
>>> appreciated.
>>>
>>> When I try to run the [vmd setup.psf -pdb zero.fep] command (step 6) in
>>> my terminal, vmd opens, but my newly created molecule does not appear. I
>>> have checked and rechecked all of my files with the example-output folder
>>> and everything is correct. I tried this same command in the VMD TkConsole,
>>> but I still don't get my new hybrid.
>>>
>>> I have the latest version of VMD and NAMD.. I don't think I need the
>>> alchemify command (I tried it anyway; it made no difference) Does anyone
>>> know what I could quite possibly be doing wrong?
>>>
>>> Regards,
>>> Alisha
>>>
>>
>>
>>
>> --
>> Chris Harrison, Ph.D.
>> NIH Center for Macromolecular Modeling and Bioinformatics
>> Theoretical and Computational Biophysics Group
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>>
>> http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078
>> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>>
>>
>>
>>
>
-- Chris Harrison, Ph.D. NIH Center for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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