Re: Two parameter file in NAMD configuration file

From: Vermaas, Joshua (
Date: Mon Jun 12 2017 - 10:20:44 CDT

Benzene has no oxygens. I suspect you added your benzene in a way that caused misassigned atomtypes. Compare the atomtypes in your cyclodextrin psf to the atomtypes in the cyclodextrin+benzene psf. You probably will notice that they are different, and this is the root of your problem.


On 06/09/2017 10:44 PM, divyabharathi korlepara wrote:
Hi Brain,

                     Whatever you told is correct. I also suspected that some oxygen vdW parameter is missing. To confirm that, i have simulated cyclodextrin with carbohydrate force field then it ran without any error. Moreover, I have oxygen atom type in cyclodextrin only so ideally it should work if we add benzene in the system also. But it is working with cyclodextrin alone. If you want I can send you the relevant files.


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On Fri, Jun 9, 2017 at 10:30 PM, Vermaas, Joshua <<>> wrote:
My money is on a bad psf with atomtypes that are not correctly specified. Atom type O would be really weird in CHARMM land, and while there isn't a force field specified, having an atomtype that pretends to be the universal oxygen atomtype is something other forcefields probably shy away from too.


On 06/09/2017 08:45 AM, Radak, Brian K wrote:

Correct me if I'm wrong, but this seems to be a pretty straightforward error message. Is there an entry for an atom type "O" in the NONBONDED section of any of the parameter files you included? If the answer is "no", then you are missing a file. If the answer is "yes", then something more serious might be happening.

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory

9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643<><<>>

From:<><<>> <<>><<>> on behalf of divyabharathi korlepara <<>><<>>
Sent: Friday, June 9, 2017 2:58 AM
Subject: namd-l: Two parameter file in NAMD configuration file

Hi NAMD users,

                      I am new to NAMD. I have to run a simulation for a system
having cyclohexane and benzene.

               I have generated psf files using charmm carbohydrate
topology for cyclodextrin and cgenff for benzene.

1) As mentioned in the given link we can use to more than one
parameter file><>

2) While running the simulation i have mentioned two
parameter files using keyword 'parameters' then the simulation terminating
by giving the

Awaiting for your response.


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