VMD-L Mailing List

From: Daan Mevius (daanmevius_at_gmail.com)
Date: Tue Oct 13 2015 - 09:23:50 CDT

Dear Richard and Pawel,
I have edited all lines and marks from the parameter file and still didn't
get it to work. However after many hours upon careful inspection (read; by
luck) i found out that i was missing one enter/return on the last line of
the parameter file and it turned out that with this added enter/return in
addition to the removal of ''!'' and comments solved my problems. Now the
the Energy minimization & Molecular dynamics finally work!
Thank you so much for the accurate and quick response!

A lesson for all (You heard it before but will not take it serious until
you spent 70 hours trying to fix it while missing such a simple mistake):
*Remove all unnecessary comments from your files, exclamation marks and
make sure to have correct enter/returns throughout your WHOLE file,
especially the last line!*

With Kind Regards
~Daan Mevius

On Sun, Oct 11, 2015 at 10:33 PM, Pawel Kedzierski <
pawel.kedzierski_at_pwr.edu.pl> wrote:

> Dear Daan,
> W dniu 11.10.2015 o 13:20, Daan Mevius pisze:
>
> Hello,
>
> I want to do Molecular Dynamics on Histone methyltransferase enzymes which
> require the S-Adenosyl-L-methionine / SAM co-factor. Therefore I have to
> generate correct Topology & Parameter files. However this has proven to be
> problematic for me. Similar questions about this compound have come up
> before and have been solved. However I still did not manage to successfully
> run my MD simulations.
>
> The SAM compound contains a cationic tricoordinate Sulphur which creates
> problems for Topology & Parameter generators such as CGenFF, Paramchem,
> SwissParam, Charmm-gui and PSFgen. All of these run into errors and do not
> provide me with correct output files.
>
> There is one paper which generously provides their Topology & Parameter
> files:
>
> ‘’Insight into Enzymatic C−F Bond Formation from QM and QM/MM Calculations
> by Hans Martin Senn
> <http://pubs.acs.org/action/doSearch?ContribStored=Senn%2C+H+M> ,*
> <http://pubs.acs.org/doi/suppl/10.1021/ja053875s#ja053875sAF1>†
> <http://pubs.acs.org/doi/suppl/10.1021/ja053875s#ja053875sAF2> David
> O'Hagan <http://pubs.acs.org/action/doSearch?ContribStored=O%27Hagan%2C+D>
> ,‡ <http://pubs.acs.org/doi/suppl/10.1021/ja053875s#ja053875sAF3> and Walter
> Thiel <http://pubs.acs.org/action/doSearch?ContribStored=Thiel%2C+W> *
> <http://pubs.acs.org/doi/suppl/10.1021/ja053875s#ja053875sAF1>†
> <http://pubs.acs.org/doi/suppl/10.1021/ja053875s#ja053875sAF2>; *J. Am.
> Chem. Soc.*, 2005, 127 (39), pp 13643–13655 *DOI:* 10.1021/ja053875s’’ (
> http://pubs.acs.org/doi/suppl/10.1021/ja053875s)
>
> With this topology file I am able to create a PSF file without any
> apparent errors (There might be a problem while creating this however, I am
> not sure about this), followed by the creation of a waterbox. However when
> I try to run Energy Minimization & Molecular dynamics using NAMD (using
> script or VMD graphical interface) I run into the same errors:
>
> FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE
> C:/Users/Daan/Documents/PhD-KNU/Correct-AdoMet/AdoMet-paper-parameters-auto.par
>
> LINE=*CN8B S 240.000 1.858 !hms: r0 from QM(aq)*
>
> The problem apparently comes from missing BONDS header in the parameter
> file. I looked up the supporting info from the link you provided and I saw
> that all the parameter section headers are commented out. You should remove
> the exclamation mark (which is a comment character in CHARMM files) in
> front of BONDS, ANGLES, DIHEDRALS and NONBONDED headers in your par file.
> I am not sure OOM but I believe that also every section should be ended
> with an empty line and that there should and END line at the end of file.
>
> Cheers,
> Pawel
>
>
>
> I included the NAMD input file and NAMD output files in the attachments in
> txt format.
>
>
> I have seen in the other posts that it might have something to do with the
> AUTOgeneration of angles and/or dihidrals, but all I have been able to find
> is the following command:
>
> AUTOgen { ANGLes [ DIHEdrals ] }
>
> { DIHEdrals [ ANGLes ] }
>
>
>
> It has also been mentioned that these files can be created using ADE, and
> the SAM Patches using the toppar files. However since my knowledge about
> this topic is limited i have unfortunately not been able to get this
> working.
>
>
> I have tried many things but have not been able to solve this problem for
> over a week. If someone here would be willing to help me that would be
> great! Thank you in advance, Daan Mevius.
>
>
>