RE: Problems to parametrize molecules

From: Bennion, Brian (
Date: Wed Apr 15 2015 - 15:44:53 CDT


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"

From: Evandro Semighini []
Sent: Wednesday, April 15, 2015 1:37 PM
To:; Bennion, Brian
Subject: Re: namd-l: Problems to parametrize molecules


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 NAMD.

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!


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

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.

It APPEARS that you are reading in the pdb file and molefacture is using that atom type.

Please list the steps that you are following and the results you get from those steps and then what you THINK those steps should have done.


From: Evandro Semighini [<>]
Sent: Wednesday, April 15, 2015 9:00 AM
To: Bennion, Brian

Subject: Re: namd-l: Problems to parametrize molecules

I got the psf from charmm_gui, but is seems that it's not working with my molecules.

I tried now with another molecule and it doesn't recognize the bond parameters between two atoms that are bonded and listed at the BOND list of psf file.

There is another way to parametrize this molecules ?

Molefacture doesn't put the partial charges and misses the correct atom types (instead of CG311 it calls C3)

Thank you

2015-04-14 17:57 GMT-03:00 Bennion, Brian <<>>:
still guessing but the psf file is not correct and that is what counts. I am not sure how you got your psf file from the pdb or mol2 but molefacture might be a plugin to use just to see the difference in the psf file that it creates compared to the current psf file.


From: Evandro Semighini [<>]
Sent: Tuesday, April 14, 2015 1:51 PM
To:<>; Bennion, Brian
Subject: Re: namd-l: Problems to parametrize molecules

Thank you Brian,

I thought that this as the problem too, but I don't know how to fix it, since the input files (pdb or mol2) have the correct bond orders.

I can change this with molefracture, before try the psfgen or the sites I tried ?

2015-04-14 17:45 GMT-03:00 Bennion, Brian <<>>:
I am just guessing here...

You need to pay attention to the what the error states. The errors suggest that the same atom is bonded to itself and it obviously cant find that in the parameter file.

From:<> [<>] on behalf of Evandro Semighini [<>]
Sent: Tuesday, April 14, 2015 1:30 PM
Subject: namd-l: Problems to parametrize molecules

Hello NAMD community

I am trying to run NAMD with the results of virtual screening assays I made, but I am not being able to parametrize the molecules properly.

I read everything I found about it but, unfortunately, it didn't worked.
I tried charmmgui and paramchem webservers to generate the psf files, but when I try to run NAMD, theres always some unknown atom type (this errors are from two different molecules)



This atom types are at the par_all36_cgenff.prm and I added all the parameter files from the package to run this simulations.
There were no high penalties for the atoms from the servers.

Can you please help me to find where I am missing or show me where I should go to parametrize this molecules for the simulations ?

Thank you,

Evandro Semighini
University of São Paulo - Brazil

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