Re: Re: Problems to parametrize molecules

From: Evandro Semighini (
Date: Sun Apr 19 2015 - 18:47:21 CDT

Hello Christopher,

Thank you !

Problem #1

Yes, I always uploaded mol2 files, I tried even to upload them converted
from diferent softwares to check if that was the problem, but it wasn't.
I am using VMD 1.9.2, as I began with NAMD this month. I prepare the files
at windows and send them to a linux server to run the simulations.

Thank you for the pgn file.

I did as you said and things gone the same way, it doesn't recognize the
UNK residue (that come like this as an output from the docking software).
So, I edited the molecule to put the residues, like is in the cgenff file
(a benzene ring, BENZ and so on), and psfgen finally runned with my
But it misses the number of atoms. The original file has 64, the psf
produced have 17.
I edited then the chains, putting each residue as one chain, and the psf
gone to 73 atoms (I guess it's adding atoms where are the bonds linking the

I'm guessing I'll have to edit the cgenff file to remove one hydrogen from
this "residues" to make it work, right ?
I also considered doing two things:
- a parameter file only with this residues, for each molecule.
- a parameter file for each molecule with the whole molecule as one
residue, and use the paremeters from the "residues", got from the cgenff
paremeter file.

I also found the some mising parameters and generated a new .par file with
fftk now.

I'll look for TopoTools, thank you.

I guess that if this ideas work, the problema #2 will be solved too.

I just received an e-mail from ParamChem about updates and I hope this
updates solves my problem or any of this tests do.

Thanks again for the help.


2015-04-17 13:16 GMT-03:00 Mayne, Christopher G <>:

> Evandro,
> Reading over the message thread, it's a little difficult to follow
> *exactly* what is going wrong, so let's take a step back here. There are
> two steps to getting simulations that include small molecules to work 1)
> generate a proper PSF/PDB file pair and 2) acquire appropriate parameters
> for any missing terms. The original error report is likely due to a
> problem in the PSF generation, since:
> 22)
> is telling you that the atom is bonded to itself. So let's address
> problem #1 first.
> I'm unfamiliar with CHARMMGUI output for small molecules, but have
> extensive experience using ParamChem. When you upload a PDB or MOL2 (mol2
> is preferred because it contains explicit bond orders useful in typing by
> analogy), it will return a CHARMM Stream file. The str file is a
> combination of topology and parameters. This stream file, along with a pdb
> of your molecule should work as expected with PSFGEN, to yield a properly
> formatted PSF. Make sure that you are using VMD 1.9.2, as PSFGEN used to
> have trouble with extended atom types like those used in CGenFF, which is
> fixed. PSFGEN can be a little tricky, so pay attention to your input and
> carefully read any output, especially warnings or errors. Here is an
> example of my commands:
> package require psfgen
> resetpsf
> psfcontext reset
> topology top_all36_cgenff.rtf
> topology my_paramchem_output.str
> segment L { first none; last none; pdb my_ligand.pdb }
> coordpdb my_ligand.pdb
> regenerate angles dihedrals
> writepsf my_ligand.psf
> Regardless of where/how you get your PSF/PDB file pair, you should
> always load the resulting structure into VMD and give it a thorough going
> over; the TopoTools commands are very useful for this. ffTK also has some
> atom labeling functions that I used to inspect atom names, types, charges,
> etc. (see ffKT -> Opt. Charges -> Input -> Label Atoms Menu).
> As for acquiring appropriate parameters, problem #2, this is a much more
> complicated issue that is discussed elsewhere. There are a variety of
> places to obtain them, e.g., ParamChem, MATCH, ffTK etc; however, I
> strongly urge you to pay attention to penalty scores (if provided) and
> consider performing some form of validation or refinement (e.g., ffTK).
> Once you have parameters, you need to use them correctly. Errors such as:
> Unable to find bond parameters for CG311 NG311 (Atoms 1 2)
> is telling you that this parameter is missing. The ParamChem webserver
> gives you two options 1) it returns only parameters which are not part of
> CGenFF standard parameter set, or 2) All parameters (i.e. novel and
> standard) required for the molecule. My guess is that you selected option
> #1 and then didn't include the standard CGenFF parameter file in your NAMD
> configuration file.
> Hopefully this information is helpful. I suggest that you revisit your
> work, pay attention to the errors that are emitted by PSFGEN/VMD/NAMD, and
> carefully think about your workflow.
> Regards,
> Christopher Mayne

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