Re: vmd-l: namd CG minimization error: unable to find angle parameters for nxg nxx nxg

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Dec 10 2009 - 15:06:05 CST

Hi Francesco,
did you directly copy/paste that error message? There shouldn't be any
beads named nxx or nxg, only Nxx and Nxg.

Also, you should always use "exclude 1-2" in rbcg simulations. There's
no such thing as scaled1-2, and the force field was not designed for use
with 1-4 exclusions.
Best,
Peter

Francesco Pietra wrote:
> I am trying to minimize at const vol a CG system
> protein-popcbilayer-water with protein and bilayer restrained. After
> adjusting the conf file on the basis of errors messages, I am getting
> an error "unable to find angle parameters for nxg nxx nxg" which I
> could not remedy although I have followed the thread with same error.
>
> The conf file
>
> # Input
> paraTypeCharmm on
> parameters /workingdir/rbcg-2007.par
>
> means that the par file is in the working dir and it contains the
> requested parameters. Is rbcg-2007.par not enough? In particular, how
> to give parameters for the POPC lipid, which are not comprised in that
> par file?
>
> But I was suspicious that the above setting of parameters is incorrect
> because if I modify
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
> to scaling 1-2 (as I have seen in a thread for CG), I get "Error: 1-2
> scaling". Which seems to me to imply that the procedure is assuming -
> from the above input -an all-atoms system.
>
> Thanks for help
>
> francesco pietra
>

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