From: Alisha \ (jonesan_at_muohio.edu)
Date: Mon Mar 19 2012 - 11:02:52 CDT
Thank you both for all of your help! That worked!
On Mar 19, 2012 3:54 AM, "JC Gumbart" <gumbart_at_ks.uiuc.edu> wrote:
> VMD doesn't know automatically that something with a *.fep extension is a
> pdb.
>
> Use this: mol addfile zero.fep type pdb
>
>
> On Mar 19, 2012, at 1:56 AM, Alisha Jonesy Jones 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
>>
>>
>>
>>
>
>
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