Re: Issue with NAMD Not understand

From: harish vashisth (harish.vashisth_at_gmail.com)
Date: Fri Nov 12 2010 - 13:57:14 CST

Hi Adrienne,
 The issue is what the error suggests: for some reason, the parameters for
the particular CN7B-HN5 bond were not found in the parameter file you
specified in the NAMD config. input file. When you used PSFGEN to generate
your pdb/psf with the help of topology you mention, the CN7-HN5 bond gets
created and if it is a new bond, there will not be any parameters for it in
any standard parameter file. Now, the topology you seem to be using will
only have information on nucleic acids, but not on your carbon
structure--because you do not mention what kind of structure that is,
whether you have topology information for that? I would suggest looking to
how pdb/psf was generated and if they were generated correctly at all or
not. Lastly, if you realize that there is no info on the bond, you can add
this type of information at appropriate place in your parameter file taking
parameters from the closest related bond in existing parameter. I hope it
helps. Other users may give some more suggestions.

On Fri, Nov 12, 2010 at 1:29 PM, <avl211_at_lehigh.edu> wrote:

> Hello,
> My name is Adrienne LaFleur and I am a senior at Lehigh University. My
> problem that I keep running into with NAMD is that when I try to run a
> simulation of a single stranded DNA of repeating thymine bases in an
> interaction with another carbon structure, NAMD will not run the simulation
> and gives the error "Can't Find Bond Parameters for Bond CN7B-HN5 in
> parameter files. The parameter files being used is par_all27_na.prm which is
> the corresponding parameter file to the topology file top_all27_na.inp. Also
> par_all27_na_lipid.prm and par_all27_prot_lipid.prm are also apart of the
> configuration file. The topology file aforementioned was used to build the
> psf file of the DNA and the carbon structure being used. So I am unaware of
> what the issue is. Thank you for your help.
> Sincerely,
> Adrienne LaFleur
>
>
>
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