From: Dr. Eddie (eackad_at_gmail.com)
Date: Sun Nov 18 2012 - 10:20:01 CST
Thanks, JC. So I take away that even if I am not using the Energy
specifically (only the dynamics: distances, rmsd etc) I need the cross
When I run some models in namd I get errors like:
*FATAL ERROR: UNABLE TO FIND CROSSTERM PARAMETERS FOR C N CP1 C N CP1
(ATOMS 11 12 13 25 15 16 17 27)*
A previous post to the list gave the following (now broken link):
as a way to update the cmap terms and thus correct the error. Where is the
most up to date protein parameter file located so I can then correct the
above problem (assuming that is the problem).
Thank you very much for your help!!
On Sat, Nov 17, 2012 at 4:24 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> I looked into this today. Stefan is using an outdated version of the
> CHARMM topology and parameters that do not have CMAP. The problem arises
> because when Mutator rebuilds the PSF file, it uses a more up-to-date
> version of the topology that adds some crossterms. When Stefan goes to the
> run the simulation with the outdated parameter file, it naturally can't
> find the appropriate values for those crossterms.
> I will mention this to Stefan.
> On Nov 16, 2012, at 1:48 PM, JC Gumbart wrote:
> This line, for example, in the log file begs to differ:
> Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
> CMAP has been in NAMD for many years now. This may be (or have been?) a
> mutator specific issue. If so, someone should check more closely that the
> plugin isn't generating additional superfluous cross terms.
> On Nov 16, 2012, at 1:15 PM, Dr. Eddie wrote:
> does namd use the cross-terms in the psf file for its calculations or is
> it ignored?
> Stefan Franzen: claims it does not
> Anyone know for sure?
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