From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Mar 18 2015 - 17:42:03 CDT
Hi Sadegh,
toppar_waters_ions_fixed.str (and the original toppar_waters_ions.str)
have NBFIX lines to correct sodium interactions with various carbonyl
oxygens, including those found in lipids and carbohydrates. NAMD
encounters these entries, sees that it doesn't know about the atomtypes
specified in the NBFIX entries, and throws the error you got. You can
either add parameter files as Jeff suggests, or comment out the
offending NBFIX entries.
-Josh Vermaas
On 3/18/15 4:35 PM, Jeff Comer wrote:
> Hi,
>
> OC2D2 is a carbohydrate type. You probably need "parameters
> par_all36_carb.prm" in your NAMD config file.
>
> Jeff
>
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Assistant Professor
> Institute of Computational Comparative Medicine
> Nanotechnology Innovation Center of Kansas State
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311
>
>
> On Wed, Mar 18, 2015 at 4:47 PM, Sadegh Faramarzi Ganjabad
> <safaramarziganjabad_at_mix.wvu.edu> wrote:
>> Hello
>>
>> I'm having an issue with NAMD configuration file, similar to link below,
>>
>> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2012-2013/3527.html
>>
>> although I put par_all36_cgenff.prm and par_all36_lipid.prm before the
>> streams files (toppar_all36_lipid_detergent.str and
>> toppar_water_ions_fixed.str). Does anybody know what
>> the problem is?
>>
>> Thanks
>> Sadegh
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