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

From: felmerino_at_uchile.cl
Date: Tue Jun 29 2010 - 20:34:07 CDT

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: petefred_at_ks.uiuc.edu

Fecha: 29-06-2010 14:17

Para: "Emily Chen"<chen2041_at_umn.edu>

CC: <namd-l_at_ks.uiuc.edu>

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:
  "FATAL ERROR: DIDN'T FIND VdW PARAMETER FOR ATOM TYPE NH3."
  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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