From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Sep 01 2017 - 16:06:53 CDT
Ahh, I see the confusion. So in Tcl, "#" is the comment character. For reasons that I'm sure made sense at the time, "!" is the comment character in parameter files, which are used extensively to tell the parser to ignore everything else on the line that might be useful for humans. So to comment out the offending lines, they should be:
!ON1 CLGR1 -0.2000 3.4000 ! NBFIX for carbonyl oxygen in nucleic acid bases
!ON1C CLGR1 -0.2000 3.4000 ! NBFIX for carbonyl oxygen in nucleic acid bases
On 09/01/2017 02:44 PM, Natasha Gupta wrote:
Ok I found the file (par_all36_cgeff.prm) but there are many lines with "!". i commented out the following lines but still recieve the same error:
#ON1 CLGR1 -0.2000 3.4000 ! NBFIX for carbonyl oxygen in nucleic acid bases
#ON1C CLGR1 -0.2000 3.4000 ! NBFIX for carbonyl oxygen in nucleic acid bases
Is this the line you are referring to comment out?
On Fri, Sep 1, 2017 at 12:36 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
Comment out the line with "!". It should be in the parameter file for the ions (grep ON1 *.prm).
On 09/01/2017 01:28 AM, Natasha Gupta wrote:
Thank you Josh - how do I correct this for NBFIX terms?
On Thursday, August 31, 2017, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov><mailto:Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>>> wrote:
Alright, upon further reflection, I hadn't considered potential NBFIX
terms for ions within the force field. If NAMD encounters an atomtype
within an NBFIX-specified interaction (such as those for ions with
carbonyls) that wasn't previously identified, this message will crop up
too. This is probably the 1% of time that I was unreasonably certain. :)
On 08/31/2017 10:29 AM, Vermaas, Joshua wrote:
> Hi Natasha,
> If NAMD is giving you that warning, I'm 99% sure that your psf file
> *does* contain ON1 somewhere. Load your psf file first, then your PDB,
> and search for "type ON1" within VMD. You'll find your atoms pretty
> quick (should be carbonyl oxygens within nucleic acids). You may have
> just not added in the nucleic acid parameters your system needs.
> On 08/31/2017 04:59 AM, Natasha Gupta wrote:
>>> I am trying to run minimization but am seeing the following error:
>>> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE ON1
>>> My psf file does not have an atom type, "ON1". Has anyone seen this before? I would appreciate any suggestions.
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