From: Zeinab Emami (zemami_at_ku.edu.tr)
Date: Mon Oct 13 2014 - 04:55:06 CDT
Dear Ashar Malik,
Thank you fro your answer, this is my pdb file:
*HETATM 1 C2 C 1 0.756 -0.045 -0.137 1.00 0.00
*
*HETATM 2 C1 C 1 -0.757 0.044 0.138 1.00 0.00
*
*HETATM 3 H3 C 1 -1.280 0.345 -0.782 1.00 0.00
*
*HETATM 4 H4 C 1 -0.943 0.788 0.926 1.00 0.00
*
*HETATM 5 H5 C 1 -1.127 -0.938 0.465 1.00 0.00
*
*HETATM 6 H6 C 1 1.105 -1.069 0.059 1.00 0.00
*
*HETATM 7 H7 C 1 1.290 0.657 0.521 1.00 0.00
*
*HETATM 8 H8 C 1 0.953 0.215 -1.188 1.00 0.00
*
ETHANE MOLECULE, [file also attached to the email].
I used autopsf for the pdb file. I took the atom names form the charmm
force field atom name list:
http://dogmans.umaryland.edu/~kenno/tutorial/par_all36_cgenff.prm
I got ethane as a sample for training in order to leran how to prepare the
parameter fiel for any given new molecule.
I am using fftk for this purpose and as soon as I have the pdb file, I
shall be able to produce the parameter file for the
given molecule.
I know many people are doing this at the moment, though I did not managed
to find a good and thorough relevant
document on the web. I would appreciate it if you guide me to a beneficial
document about this.
Sincerely,
Zeinab
On Mon, Oct 13, 2014 at 12:40 PM, Ashar Malik <asharjm_at_gmail.com> wrote:
> Hi,
>
> Could you send me the PDB file that you are using to generate the PSF
> file. I will try looking at it and if I can let you know what is causing
> the problem.
>
> Also mention what force field are you using to generate the PSF file.
>
> The more information you provide - the quicker you will get your answer.
>
> Best,
> /A
>
> On Mon, Oct 13, 2014 at 10:00 PM, Zeinab Emami <zemami_at_ku.edu.tr> 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/
>>>>
>>>>
>>>>
>>>
>>>
>>
>
>
> --
> Best,
> /A
>
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