VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Sat Nov 08 2014 - 11:29:31 CST

Zeinab,

I think you are confusing topology and parameter files. They contain different information, and I refer you to the Appendices of the NAMD tutorial for descriptions of these file contents (http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/index.html).

Structure building and its relationship to parameterization is not for the meek, and to be successful you must take the time to gain a firm understanding of all pieces. For generation of PSF/PDB files, I refer you back to our previous discussion (http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/24513.html) regarding how to generate PSF/PDB files pairs for small molecules. Molefacture can also help one set name, type, charge, and connectivities to yield PSF/PDBs.

If there are features that have changed between VMD versions that you must have, you can maintain two different copies of VMD without conflict (no need to uninstall/reinstall).

Let's move any future discussions regarding Molefacture into a new thread with a subject line that represents that content, as it is no longer an ffTK issue.

Regards,
Christopher Mayne

On Nov 8, 2014, at 10:30 AM, Zeinab Emami wrote:

No, I unistalled vmd 1.9.2 and installed VMD 1.9.1. Because in the molfacture plugin of VMD 1.9.1, there is an option that when the user is finished with changing the atom names, types and charges and is going to write the PSF and PDB file, s/he can brows any parameter file.

Since the molcules we intend to inspect are new and complicated, they are not included in C27 which is default of VMD. Therefore, I assumed that we will be able to solve this defficiency by loading par_all36_cgenff while writing pdb and psf files in molefacture. I tried this for two different ligand [29 and 54 atoms] ;it did not work.

As a second try, following the recommendation of a vmd expert, I typed the pathway of all the par and top files of C36 in a text file, proceeding each line with STREAM:

stream C:\Users\zemami\Desktop\ETHA\toppar\00toppar_file_format
stream C:\Users\zemami\Desktop\ETHA\toppar\par_all22_prot.prm
stream C:\Users\zemami\Desktop\ETHA\toppar\par_all35_ethers.prm
stream C:\Users\zemami\Desktop\ETHA\toppar\par_all36_carb.prm
stream C:\Users\zemami\Desktop\ETHA\toppar\par_all36_cgenff.prm
stream C:\Users\zemami\Desktop\ETHA\toppar\par_all36_lipid.prm
stream C:\Users\zemami\Desktop\ETHA\toppar\par_all36_na.prm
stream C:\Users\zemami\Desktop\ETHA\toppar\par_all36_prot.prm
stream C:\Users\zemami\Desktop\ETHA\toppar\par_hbond.inp
stream C:\Users\zemami\Desktop\ETHA\toppar\param19.inp
stream C:\Users\zemami\Desktop\ETHA\toppar\top_all22_prot
stream C:\Users\zemami\Desktop\ETHA\toppar\top_all35_ethers
stream C:\Users\zemami\Desktop\ETHA\toppar\top_all36_carb
stream C:\Users\zemami\Desktop\ETHA\toppar\top_all36_cgenff
stream C:\Users\zemami\Desktop\ETHA\toppar\top_all36_lipid
stream C:\Users\zemami\Desktop\ETHA\toppar\top_all36_na
stream C:\Users\zemami\Desktop\ETHA\toppar\top_all36_prot
stream C:\Users\zemami\Desktop\ETHA\toppar\toph19.inp
stream C:\Users\zemami\Desktop\ETHA\toppar\toppar_all.history
stream C:\Users\zemami\Desktop\ETHA\toppar\toppar_water_ions.str

And in the molefacture write pdb and psf file, in parameter file brows, I loaded this text file. this way also did not work.

I wrote all these to:

1. explain why we switched from vmd 1.9.2 to vmd 1.9.1.
2 to get advise from you about our problem with molefacture for complicated compunds.

Sincerely Yours,
Zeinab

On Sat, Nov 8, 2014 at 6:11 PM, Mayne, Christopher G <cmayne2_at_illinois.edu<mailto:cmayne2_at_illinois.edu>> wrote:
Zeinab,

Are you using the latest release of VMD 1.9.2?

Following the conversation to the threads you linked previously...
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21652.html

Regards,
Christopher Mayne

On Nov 8, 2014, at 7:40 AM, Zeinab Emami wrote:

Dear Christopher G Mayne,

I am getting the same error as Wenhao and Esra Bozkurt while running charge optimization:

error deleting "base-wat.pdb": permission denied
error deleting "base-wat.pdb": permission denied
    while executing
"file delete base-wat.pdb"
    (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 125)
    invoked from within
"::ForceFieldToolKit::ChargeOpt::optimize"
    (procedure "::ForceFieldToolKit::gui::coptRunOpt" line 55)
    invoked from within
"::ForceFieldToolKit::gui::coptRunOpt "
    invoked from within
".fftk_gui.hlf.nb.chargeopt.runOpt invoke "
    invoked from within
".fftk_gui.hlf.nb.chargeopt.runOpt instate {pressed !disabled} { .fftk_gui.hlf.nb.chargeopt.runOpt state !pressed; .fftk_gui.hlf.nb.chargeopt.runOpt in..."
    (command bound to event)

[http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21646.html
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21195.html]

I read your suggestion to Wenhao [cd to a local directory in which you have read/write privileges, and rerun the optimization.] I was already in the directory which contains all files concerning ffTK on my own P.C.

Sincerely Yours,
Zeinab