VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Oct 20 2014 - 14:19:29 CDT

The screencasts were made quite awhile ago. Since then I have made several improvements and small changes to the GUI, although one should generally still be able to use the screencasts as a guide. If you are using the 1.9.2 beta, you should enter the location of PSF and PDB and then click "Analyze". This will load the molecule and fill out the boxes beneath it with missing parameters that will allow you to visualize the parameters in the VMD OpenGL window. After performing the analysis, input your desired output file path and name and click the "Write Initial Parameter File", which performs the write. If you are skipping the "Analyze" button, then you will likely write nothing to the parameter file.

Christopher Mayne

On Oct 20, 2014, at 2:14 PM, Zeinab Emami 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<mailto: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<mailto: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<mailto:mayne_at_ks.uiuc.edu>
!
! James C. Gumbart
! Georgia Institute of Technology
! http://simbac.gatech.edu>
! gumbart_physics.gatech.edu<http://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<mailto: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<mailto:mayne_at_ks.uiuc.edu>
!
! James C. Gumbart
! Georgia Institute of Technology
! http://simbac.gatech.edu>
! gumbart_physics.gatech.edu<http://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<mailto: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>