VMD-L Mailing List

From: Zeinab Emami (zemami_at_ku.edu.tr)
Date: Mon Oct 20 2014 - 14:15:16 CDT

Yes, I am using VMD1.9.2beta1.

On Mon, Oct 20, 2014 at 10:14 PM, Zeinab Emami <zemami_at_ku.edu.tr> wrote:

> Dear Christopher Mayne,
>
> I just tried it again. Still the initial parameter file I get is mere
> comments. Although there is a very subtle difference in my fftk with that
> in the video. To get the parameter fil, when I click on "identify missing
> parameters", there appears two boxes where I should upload pdb and psf
> files both, while in the video, there is only one box for uploading the psf
> file and pdb file is not uploaded.
> My laptop is 64 bit and I installed a 32 bit VMD. Could this be for that?
>
> Sincerely Yours,
> Zeinab
>
> On Mon, Oct 20, 2014 at 10:02 PM, Zeinab Emami <zemami_at_ku.edu.tr> wrote:
>
>> Dear Christopher,
>>
>> We tried it several times! I will try it again now. Thank you. It was a
>> good news to know that it works.
>>
>> Best Regards,
>> ZE
>>
>>
>> On Mon, Oct 20, 2014 at 9:50 PM, Mayne, Christopher G <
>> cmayne2_at_illinois.edu> wrote:
>>
>>> Zeinab,
>>>
>>> It works as expected for me. The contents of my output parameter file
>>> are as below.
>>>
>>> Christopher Mayne
>>>
>>> !=============================================================
>>> !
>>> ! Parameter file generated by the Force Field ToolKit (ffTK)
>>> !
>>> ! For additional information, see:
>>> ! http://www.ks.uiuc.edu/Research/vmd/plugins/fftk
>>> ! http://www.ks.uiuc.edu/Research/fftk
>>> !
>>> ! Authors:
>>> ! Christopher G. Mayne
>>> ! Beckman Institute for Advanced Science and Technology
>>> ! University of Illinois, Urbana-Champaign
>>> ! http://www.ks.uiuc.edu/~mayne
>>> ! mayne_at_ks.uiuc.edu
>>> !
>>> ! James C. Gumbart
>>> ! Georgia Institute of Technology
>>> ! http://simbac.gatech.edu
>>> ! gumbart_physics.gatech.edu
>>> !
>>> ! If you use parameters developed using ffTK, please cite:
>>> ! C.G. Mayne, J. Saam, K. Schulten, E. Tajkhorshid, J.C. Gumbart. J.
>>> Comput. Chem. 2013, 34, 2757-2770.
>>> !
>>> !=============================================================
>>>
>>> BONDS
>>> !V(bond) = Kb(b - b0)**2
>>> !
>>> !Kb: kcal/mole/A**2
>>> !b0: A
>>> !
>>> !atom type Kb b0
>>> !
>>> CG331 HGA3 0.000 0.000
>>> CG331 CG331 0.000 0.000
>>>
>>> ANGLES
>>> !
>>> !V(angle) = Ktheta(Theta - Theta0)**2
>>> !
>>> !V(Urey-Bradley) = Kub(S - S0)**2
>>> !
>>> !Ktheta: kcal/mole/rad**2
>>> !Theta0: degrees
>>> !Kub: kcal/mole/A**2 (Urey-Bradley)
>>> !S0: A
>>> !
>>> !atom types Ktheta Theta0 Kub S0
>>> !
>>> !
>>> CG331 CG331 HGA3 0.000 0.000
>>> HGA3 CG331 HGA3 0.000 0.000
>>>
>>> DIHEDRALS
>>> !
>>> !V(dihedral) = Kchi(1 + cos(n(chi) - delta))
>>> !
>>> !Kchi: kcal/mole
>>> !n: multiplicity
>>> !delta: degrees
>>> !
>>> !atom types Kchi n delta
>>> !
>>> HGA3 CG331 CG331 HGA3 0.0000 1 0.00
>>>
>>> IMPROPER
>>> !
>>> !V(improper) = Kpsi(psi - psi0)**2
>>> !
>>> !Kpsi: kcal/mole/rad**2
>>> !psi0: degrees
>>> !note that the second column of numbers (0) is ignored
>>> !
>>> !atom types Kpsi psi0
>>> !
>>>
>>> NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
>>> cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
>>> !
>>> !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
>>> !
>>> !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
>>> !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
>>> !
>>> !atom ignored epsilon Rmin/2 ignored eps,1-4
>>> Rmin/2,1-4
>>> !
>>> CG331 0.0 0.000000 0.000000 ! SET BY ANALOGY!!!
>>> HGA3 0.0 0.000000 0.000000 ! SET BY ANALOGY!!!
>>>
>>> END
>>>
>>> On Oct 20, 2014, at 1:44 PM, Zeinab Emami wrote:
>>>
>>> Sure,
>>>
>>> Ethane_e is the pdb file that we first loaded to VMD and ETHA pdb and
>>> psf files are the files we get after modifying atom names, charges and
>>> types in molefacture.
>>>
>>> Sincerely,
>>>
>>> On Mon, Oct 20, 2014 at 9:05 PM, Mayne, Christopher G <
>>> cmayne2_at_illinois.edu> wrote:
>>>
>>>> Zeinab,
>>>>
>>>> Please attach your PSF and PDB files and I will take a look at them.
>>>>
>>>>
>>>> Christopher Mayne
>>>>
>>>>
>>>> On Oct 20, 2014, at 12:44 PM, Zeinab Emami wrote:
>>>>
>>>> Dear Christopher Mayne,
>>>>
>>>> I read your answer:
>>>>
>>>> I should specify that in the screencast tutorials we did not include
>>>> the standard CGenFF parameter file as the "associated parameter file"
>>>> because we wanted to treat pyrrolidine as if it were completely unknown (it
>>>> is included in the standard CGenFF files). When building the initialized
>>>> parameter file, ffTK first determines all of the parameters needed to
>>>> describe the molecule (using the information in the PSF), and then
>>>> crosschecks these required parameters against any parameter sets listed as
>>>> "associated parameter files." ffTK will only write out the parameters that
>>>> it does not find. In this case, if you included the CGenFF parameter file,
>>>> ffTK will find all of the parameters it is looking for and will generate an
>>>> empty parameter file.
>>>>
>>>>
>>>> The matter is that, we are at the phase pf learning. Therefore, we
>>>> want to know how ffTK works for a completely unknown molecule. In that
>>>> case, we expect to get an initial parameter file with the initial values
>>>> [for bonds, angel..] all set to zero. But the initial parameter file we get
>>>> from the first step in ffTK is oddly void of any atom, and it contains only
>>>> comments. The file content is pasted below.
>>>>
>>>>
>>>> Best Regards,
>>>> Zeinab
>>>>
>>>>
>>>> !=============================================================
>>>> !
>>>> ! Parameter file generated by the Force Field ToolKit (ffTK)
>>>> !
>>>> ! For additional information, see:
>>>> ! http://www.ks.uiuc.edu/Research/vmd/plugins/fftk
>>>> ! http://www.ks.uiuc.edu/Research/fftk
>>>> !
>>>> ! Authors:
>>>> ! Christopher G. Mayne
>>>> ! Beckman Institute for Advanced Science and Technology
>>>> ! University of Illinois, Urbana-Champaign
>>>> ! http://www.ks.uiuc.edu/~mayne
>>>> ! mayne_at_ks.uiuc.edu
>>>> !
>>>> ! James C. Gumbart
>>>> ! Georgia Institute of Technology
>>>> ! http://simbac.gatech.edu
>>>> ! gumbart_physics.gatech.edu
>>>> !
>>>> ! If you use parameters developed using ffTK, please cite:
>>>> ! C.G. Mayne, J. Saam, K. Schulten, E. Tajkhorshid, J.C. Gumbart. J.
>>>> Comput. Chem. 2013, 34, 2757-2770.
>>>> !
>>>> !=============================================================
>>>>
>>>> BONDS
>>>> !V(bond) = Kb(b - b0)**2
>>>> !
>>>> !Kb: kcal/mole/A**2
>>>> !b0: A
>>>> !
>>>> !atom type Kb b0
>>>> !
>>>>
>>>> ANGLES
>>>> !
>>>> !V(angle) = Ktheta(Theta - Theta0)**2
>>>> !
>>>> !V(Urey-Bradley) = Kub(S - S0)**2
>>>> !
>>>> !Ktheta: kcal/mole/rad**2
>>>> !Theta0: degrees
>>>> !Kub: kcal/mole/A**2 (Urey-Bradley)
>>>> !S0: A
>>>> !
>>>> !atom types Ktheta Theta0 Kub S0
>>>> !
>>>> !
>>>>
>>>> DIHEDRALS
>>>> !
>>>> !V(dihedral) = Kchi(1 + cos(n(chi) - delta))
>>>> !
>>>> !Kchi: kcal/mole
>>>> !n: multiplicity
>>>> !delta: degrees
>>>> !
>>>> !atom types Kchi n delta
>>>> !
>>>>
>>>> IMPROPER
>>>> !
>>>> !V(improper) = Kpsi(psi - psi0)**2
>>>> !
>>>> !Kpsi: kcal/mole/rad**2
>>>> !psi0: degrees
>>>> !note that the second column of numbers (0) is ignored
>>>> !
>>>> !atom types Kpsi psi0
>>>> !
>>>>
>>>> NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
>>>> cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
>>>> !
>>>> !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
>>>> !
>>>> !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
>>>> !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
>>>> !
>>>> !atom ignored epsilon Rmin/2 ignored eps,1-4
>>>> Rmin/2,1-4
>>>> !
>>>>
>>>> END
>>>>
>>>>
>>>>
>>>> On Mon, Oct 20, 2014 at 7:34 PM, Zeinab Emami <zemami_at_ku.edu.tr> wrote:
>>>>
>>>>>
>>>>> Hello,
>>>>>
>>>>> I am trying to test production of parameter files following the
>>>>> molefacture
>>>>> tutorial and these video series about ffTK:
>>>>>
>>>>> http://www.ks.uiuc.edu/Research/vmd/minitutorials/fftk/
>>>>>
>>>>>
>>>>> http://www.ks.uiuc.edu/Training/Tutorials/vmd-molefacture/tutorial-Molefacture.pdf
>>>>>
>>>>>
>>>>> I loaded my molecule to VMD, then invoked molefacture, edited the atom
>>>>> names, charges and type. then using "file/ write psf and pdb file"
>>>>> produced
>>>>> the psf and pdb files I need for the ffTK procedure. [VIDEO 1]
>>>>>
>>>>> Then, I loaded the psf and pdb file in fftk/BuildPar/Identify Missing
>>>>> Parameters and produced the parameter file, as it is described in the
>>>>> video
>>>>> 2.
>>>>>
>>>>> The proper parameter file, as shown in video 2, should contain the
>>>>> atoms
>>>>> and the values for bonds, angles and so on; and the values are set to
>>>>> zero.
>>>>> Although, in the parameter file I got, there is no value, just
>>>>> comments; it
>>>>> seems to me that VMD cannot read the pdb and psf files produced by
>>>>> molefacture.
>>>>>
>>>>> I hope these info are enough.
>>>>>
>>>>> Best Regards,
>>>>> ZE
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>> <ETHA.pdb><ETHA.psf><ETHA.top><Ethane_e.pdb>
>>>
>>>
>>>
>>
>