Re: Problems to parametrize molecules

From: Evandro Semighini (
Date: Thu Apr 16 2015 - 14:53:54 CDT


I'm using NAMD 2.10.
I searched and found this threads:

I changed the first line of the psf file to put the NAMD CMAP terms but
things goes the same way as before.
I tried with 4 diferent molecules and all of them get some bond or vdW

I tried to generate the prm and rtf files with MATCH, I was able to run
psfgen with it, but I got vdW errors.

As far as I saw with the ParamChem and VegaZZ, the softwares are not
recognizing the "UNK" residue.

I'm guessing I'll have to follow the "how to parametrize new ligands"
tutorial and split my molecules into "residues", draw them, put the data
from ParamChem and see if it works. Do you think it can work, without the
need of Spartan ?

FFtk asks me to use Gaussian, which I also don't have.

I'm sorry if I look lame, but I'm completely lost.

Thank you for the help.


2015-04-15 17:44 GMT-03:00 Bennion, Brian <>:

> Hello,
> which version namd are you using. searching the vmd-l list or namd-l
> should show that you need to put the key word, NAMD, in the psf file so
> that namd can accept the large atom types.
> If you get large errors from the website for your molecule,
> then FFTK in VMD is the only real way to get viable parameters.
> A great paper to MEMORIZE is mayne et al. 2013 journal of computational
> chemistry " Rapid parameterization of small molecules using the force field
> toolkit"
> Brian
> ------------------------------
> *From:* Evandro Semighini []
> *Sent:* Wednesday, April 15, 2015 1:37 PM
> *To:*; Bennion, Brian
> *Subject:* Re: namd-l: Problems to parametrize molecules
> Hello,
> I generated the pdb and psf with charmm_gui and solvated the system with
> water only, with the solvate package.
> I tried this and there is the error "Unable to find bond parameters for
> CG311 NG311 (Atoms 1 2)", which are bonded in the psf file.
> I tried then to open the molecule and edit it with molefacture,
> correcting the atom types, because it misses it, like you said.
> I also corrected the double bonds (this one missing is simple) and saved
> the molecule, solvated it and the same error shows up when I try to run
> I tried also to parametrize the molecule with paramchem, but when I try
> to generate the psf file, as described here:
> I doesn't recognize the topology files of charmm36. (any of them)
> There is any other method/program to parametrize the molecules?
> Thank you again, Brian!
> Evandro
> 2015-04-15 15:04 GMT-03:00 Bennion, Brian <>:
>> Hello,
>> can you state how you used the molefacture plugin. I need to know what
>> steps you are applying to solve this problem, EXACTLY.
>> Molefacture will not automatically assign partial charges and in cases
>> where the atom type is larger than 4 characters it will cut off the rest--047d7b41cdb8df069e0513dcd2b1--

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