Re: "didn't find VdW parameter for atom type NH3" error

From: Peter Freddolino (
Date: Tue Jun 29 2010 - 22:02:21 CDT

Dear Felipe,
As Emily can confirm, she had initially posted an all atom psf by
mistake, but then replaced it with the correct CG psf. I can, believe it
or not, distinguish between an all atom and residue-based CG psf.

On 06/29/2010 09:34 PM, wrote:
> I beg to disagree with peter, but it is a CG psf file. It uses the
> residue based coarse grain. Yet, NH3 is the atom type in the N-term of
> proteins and there is no reference to a NH3 atom in your psf. It seems
> that you have somehow confused some CG with all atom structures.
> PS: If you are using the parameters set that cames with vmd remember
> that this model was in principle parametrized in a way that it
> preserves secondary structure elements (mostly helices) very, well but
> the same is not necessarily true for terciary contacts. In our lab we
> have seen that the dihedral basin for helices (look the parameters
> file) is overestimated and you may need to create an ad hoc set of
> dihedral parameters for your specific case.
> best
> felipe
> ----Mensaje original----
> De:
> Fecha: 29-06-2010 14:17
> Para: "Emily Chen"<>
> CC: <>
> Asunto: Re: namd-l: "didn't find VdW parameter for atom type NH3"
> error
> This is not a CG psf...
> Best,
> Peter
> On 06/29/2010 08:06 AM, Emily Chen wrote:
>> Hi,
>> I'm new to NAMD. I am trying to run a coarse grained simulation,
>> but I keep getting back this error:
>> I looked in the FAQ, which suggested adding name="MAIN" at the
>> segment statement but I'm not sure what that means. I tried
>> typing in the commands in the psfgen guide
>> <> (modified
>> to fit my files) but I got errors.
>> The .conf, <>
>> parameter,
>> <> and part of
>> the psf <> I
>> used, as well as one of the .log
>> <> files it
>> put out.
>> Thank you!
>> Emily

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