From: Pawel Kedzierski (
Date: Sun Oct 11 2015 - 08:33:33 CDT

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
> <> ,*
> <>†
> <> David
> O'Hagan
> <> ,‡
> <> and
> Walter Thiel
> <> *
> <>†
> <>; /J.
> Am. Chem. Soc./, 2005, 127 (39), pp 13643–13655
> *DOI:* 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:
> 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.


> 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.