Re: Two parameter file in NAMD configuration file

From: divyabharathi korlepara (divyabharathik938_at_gmail.com)
Date: Wed Jun 14 2017 - 00:01:04 CDT

Hi,

                 Thanks for your suggestion.

                 I have simulated benzene+cyclodextrin with a parameter
file contains parameters for benzene and cyclodextrin then it works.

                 I have created the present parameter file by keeping the
parameters relevant to the benzene in carbohydrate force field then it
works.

                 So, I think their is no problem in the psf or pdb or
parameter file.

                 Exactly, I don't know what is the problem by specifying
the two parameter files.

Thanks,
Divya.

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On Mon, Jun 12, 2017 at 8:50 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> 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.
>
> -Josh
>
> 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.
>
>
>
> Thanks.
> Divya.
>
>
>
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> On Fri, Jun 9, 2017 at 10:30 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<
> mailto:Joshua.Vermaas_at_nrel.gov>> 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.
>
> -Josh
>
> 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
> brian.radak_at_anl.gov<mailto:brian.radak_at_anl.gov><mailto:brian.radak_at_anl.gov
> <mailto:brian.radak_at_anl.gov>>
>
>
> ________________________________
> From: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu><mailto:
> owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>> <
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> owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>> on behalf of
> divyabharathi korlepara <divyabharathik938_at_gmail.com<mailto:
> divyabharathik938_at_gmail.com>><mailto:divyabharathik938_at_gmail.com<mailto:
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> Sent: Friday, June 9, 2017 2:58 AM
> To: namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu><mailto:namd-l@
> ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>>
> 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
>
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> 2) While running the simulation i have mentioned two
> parameter files using keyword 'parameters' then the simulation terminating
> by giving the
> error FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE O
>
>
>
> Awaiting for your response.
>
>
> Thanks,
> Divya.
>
>
>
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