VMD-L Mailing List

From: Jernej Zidar (jernej.zidar_at_gmail.com)
Date: Tue Mar 29 2011 - 02:16:54 CDT

Hi.
  If you're talking about a regular protein or lipid, I advise you to go the portal www.charmming.org where you can easily convert a PDB file into a PSF file and COR file (just coordinates).

  I've used the portal time and again without any problem.

Best regards,
Jernej Zidar

On 28.3.2011, at 22:52, John Stone wrote:

>
> Donovan,
> The PSF file format is very verbose. Every atom, bond, etc, is explicitly
> specified, and there's no provision for replicating identical pieces of
> substructure. If you load up a PDB file in VMD and then use the
> AutoPSF plugin to generate a PSF file for it, you'll see what a more
> complex example looks like. You can read the source code for the
> VMD PSF reader/writer plugin here:
> http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/psfplugin_8c-source.html
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Mar 28, 2011 at 02:26:36PM +0100, Donovan B.T. wrote:
>> Hi All
>>
>> I've had a crack at this, but am having trouble with the .psf file format. I'm not sure that the conversion tool [top2psf] is coping with the .top file and its three .itn include files. I have tried numerous work around's for include files [but pulling them out into the .top file], but I cannot seem to find a way to get the .psf, .gro and .xtc formats all loaded correctly into VMD. Native conversion of the .top [includes extracted] into .psf doesn't work and nor does converting each .itp file individually and concatenating.
>>
>> The biggest hurdle is finding a suitable script for how I should format the .psf file, for example I have lipids and a solvent. Do I have to describe each and everyone of the lipids in the system and the same question to the solvent. Apologies for the ask, but I could find nothing other than quite simple molecules with no solvent as examples for .psf.
>>
>> Best wishes and thanks
>>
>>
>> Brett
>>
>> ________________________________________
>> From: John Stone [johns_at_ks.uiuc.edu]
>> Sent: Friday, March 25, 2011 2:11 PM
>> To: Donovan B.T.
>> Cc: Pawe? K?dzierski; vmd-l_at_ks.uiuc.edu
>> Subject: Re: vmd-l: measure dipole
>>
>> Hi,
>> VMD doesn't compute partial charges, as these are normally
>> provided by the force field your simulation is based on, and in most
>> cases you would get the charge information into VMD by loading it from
>> a file format that includes it. If you were using NAMD/CHARMM, that would
>> be from a PSF file. I believe there was a script called "top2psf" for
>> Gromacs that generates a PSF file from a .top file. I don't know how
>> well it works, but it might give you the charge information that is
>> not included in the XTC and GRO files.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Fri, Mar 25, 2011 at 01:18:38PM +0000, Donovan B.T. wrote:
>>> Hmm, I seem not be pulling out any charge information at all.
>>>
>>>>> set selatoms [atomselect top "name OW and (resid 129)"]
>>>>> $selatoms get charge
>>> 0.0
>>>
>>> This should be a oxygen atom on a water. There seem to be no partial charges at all. There are .gro and .xtc files [not my simulations] used to create the VMD render . Is VMD not computing the partial charges on the atoms??
>>>
>>> Thanks
>>> ________________________________________
>>> From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Pawe? K?dzierski [pawel.kedzierski_at_pwr.wroc.pl]
>>> Sent: Friday, March 25, 2011 7:55 AM
>>> To: vmd-l_at_ks.uiuc.edu
>>> Subject: Re: vmd-l: measure dipole
>>>
>>> On 24.03.2011 19:07, Donovan B.T. wrote:
>>>> Getting measure dipole to work.
>>>>
>>>> I have a membrane system with water and I want to select a region and compute the dipole moment at that region. For a test case I tried just a single lipid, where this is selected as follows:
>>>>
>>>>
>>>>>> set sel [atomselect top "resid 1"]
>>>>>> $sel get name
>>>>>>
>>>> gives....
>>>>
>>>> C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 O17......etc etc
>>>>
>>>> now using
>>>>
>>>>>> measure dipole $sel
>>>>>>
>>>> 0.0 0.0 0.0
>>>>
>>> This may be too obvious, but have you checked this?:
>>>
>>> $sel get charge
>>>
>>>
>>>> and does this no matter what the molecule is including water. I'm not getting any measured vector for the measured dipole. It's probably something simple. Am I doing this the best way? I'm using the whole molecule as a test initially.
>>>>
>>>> Thanks
>>>>
>>>>
>>
>> --
>> 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