VMD-L Mailing List

From: Zeinab Emami (zemami_at_ku.edu.tr)
Date: Mon Oct 13 2014 - 12:59:36 CDT

Dear Josh Vermaas,

You are right. I intended to produce psf file for a pdb file of molecule
which is not defined in the parameter files which are already defined.
Therefore, I will not try autopsf fora that anymore. thank you for your
rigorous comment.

Sincerely,
Zeinab

On Mon, Oct 13, 2014 at 5:23 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> Hi Zeinab,
>
> PDBs don't contain charge or atom type information, so I wouldn't expect
> those to change at all. Do you have a topology file for your structure? If
> not, why are you expecting autopsf to do anything useful? What Chris was
> trying to guide you through was what he does for his small molecules where
> topology files don't exist, and you'll note that he doesn't call autopsf a
> single time. The most useful documentation you will find quickly is
> re-reading Chris's reponse, unless you feel inclined to write your own
> topology file so that autopsf is useful again.
>
> -Josh Vermaas
>
>
> On 10/13/2014 04:00 AM, Zeinab Emami wrote:
>
> Dear Christopher Mayne,
>
> First, I like to thank you again for your informative answer to my
> question about producing psf file when getting the error of "Need to have
> at least one atom in your selection!".
>
> I tried your guideline and changed the names, types and charges of each
> atom in the pdb file. Though
>
> - when I change every parameter [atom name, atom type, atom charge], NO
> CHANGE AT ALL is visible in the output pdb file but in the atom names.
>
> - Although the atom names change, the problem resists and I get the same
> error when I use autopsf.
>
> I really don't expect you to tell me the last answer. I tried to search
> for a solution but failed. If you guide me to a useful document about this
> I would be grateful.
>
> Sincerely,
> Zeinab
>
> On Thu, Oct 2, 2014 at 7:03 PM, Mayne, Christopher G <cmayne2_at_illinois.edu
> > wrote:
>
>> Zeinab,
>>
>> Please cc VMD-L so that others can learn from the discussion.
>>
>> Hand editing PDB or PSF files is generally a bad idea. These formats
>> are technically adhere to fixed-width specifications such that minor
>> mistakes can easily result in broken files. My workflow in VMD typically
>> looks like this:
>>
>> 1) load the PDB file into VMD
>>
>> 2) use VMD's atomselection mechanisms to modify atom name, type,
>> charge, etc for each atom
>> e.g.,
>> set sel [atomselect top "index 0"]
>> $sel set name C1
>> $sel set type CG2R61
>> $sel set charge -0.115
>> $sel delete
>>
>> 3) check that VMD has correctly identified bonds. If it has made a
>> mistake, use the "topo addbond <id1> <id2>" or "topo delbond <id1> <id2>"
>> to fix the connectivity
>>
>> 4) once bonds are correctly defined, angles and dihedrals can
>> automatically be determined via
>> topo guessangles
>> topo guessdihedrals
>>
>> 5) If you have any impropers, it is best to add those manually,
>> although topotools can make a guess
>> topo addimproper <id1> <id2> <id3> <id4>
>>
>> 6) make sure you set the resname, chain, and segname as desired
>>
>> 7) tell VMD to update the topology
>> mol reanalyze top
>>
>> 8) write the psf/pdb
>> [atomselect top all] writepsf mymol.psf
>> [atomselect top all] writepdb mymol.pdb
>>
>>
>> typing "topo" with no arguments in VMD's tkcon will print an extensive
>> usage message
>>
>> Regards,
>> Christopher Mayne
>>
>> On Oct 2, 2014, at 5:42 AM, Zeinab Emami wrote:
>>
>> Dear Christopher Mayne,
>>
>> I have the same problem. I tried to follow you advise, though could not
>> figure out how it wors up to now. The tutorial seems not comprehensive.
>>
>> I also read this page:
>> http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/ which did not
>> help much as well.
>>
>> Would you please give me a short hint on *the procedure for producing
>> PSF file from a given pdb file that is void of parameter info.*
>>
>> E.G. I tried to modify this pdb file for ethane, in order to get its
>> psf file:
>>
>> HETATM 1 C 0 -0.772 0.000 -0.000
>> C
>> HETATM 2 C 0 0.772 0.000 -0.000
>> C
>> HETATM 3 H 0 1.179 1.012 -0.083
>> H
>> HETATM 4 H 0 1.178 -0.578 -0.835
>> H
>> HETATM 5 H 0 1.178 -0.434 0.918
>> H
>> HETATM 6 H 0 -1.178 -0.432 0.919
>> H
>> HETATM 7 H 0 -1.178 -0.580 -0.834
>> H
>> HETATM 8 H 0 -1.179 1.012 -0.086
>> H
>> END
>>
>> I changed the atom names and type manually, and the charges as well, it
>> did not work.
>>
>> I thank you in advance and look forward to hear your advise.
>>
>> Sincerely,
>> Zeinab
>>
>> On Wed, Oct 1, 2014 at 5:51 PM, Mayne, Christopher G <
>> cmayne2_at_illinois.edu> wrote:
>>
>>> MK,
>>>
>>> If you have the mol2 and/or VMD's automated bond detection is correct,
>>> you can use the TopoTools plugin (
>>> https://sites.google.com/site/akohlmey/software/topotools) all of the
>>> bonded elements found in a PSF (e.g., bonds, angles, dihedrals). TopoTools
>>> has a function for guessing impropers, but it is better to set those
>>> manually where required. I frequently use this technique to construct PSF
>>> files for small molecule ligands from PDB files. If not included in your
>>> input, you will also need to manually set the atom types and partial
>>> charges using VMD's atom selection language.
>>>
>>> Regards,
>>> Christopher Mayne
>>>
>>> On Oct 1, 2014, at 8:02 AM, John Stone wrote:
>>>
>>> Hi,
>>> If you have a mol2 file with bond information, you may not
>>> really even need a PSF file if you're just wanting to analyze it in VMD.
>>> You don't say what it is that you want to analyze, so it's hard to make
>>> any concrete statements about what you would be missing if you just
>>> proceeded using the mol2 file. If you can be more specific about your
>>> goals it would be easier to give further guidance.
>>>
>>> Cheers,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Wed, Oct 01, 2014 at 10:53:14PM +1000, M Karim wrote:
>>>
>>> Hi,
>>>
>>> I have a structure that doesn't have a psf file for it. It is not a
>>>
>>> biological material (Nucleic Acid or Protein, so I think Automatic psf
>>>
>>> builder does not work for it) I have the xyz, pdb, and mol2 as well as
>>> the
>>>
>>> trajectory files for it.
>>>
>>> How can we make the psf file for this structure to better analyze it in
>>>
>>> VMD?
>>>
>>>
>>> Thank you
>>>
>>> MK
>>>
>>>
>>> --
>>> NIH Center for Macromolecular Modeling and Bioinformatics
>>> Beckman Institute for Advanced Science and Technology
>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>>> http://www.ks.uiuc.edu/Research/vmd/
>>>
>>>
>>>
>>
>>
>
>