Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon May 16 2016 - 08:54:31 CDT

Dear Peter:
yes, I made that clear. Apparently, to my disappointment, NNEU was not
accompanied by appropriate parameters for atom C being terminal.

all the best
francesco

On Mon, May 16, 2016 at 2:46 PM, Peter Freddolino <petefred_at_umich.edu>
wrote:

> Dear Francesco,
> The lines that you quoted from the prm file are for angles centered on CC,
> but the angle that namd is complaining about is centered on CT1. These are
> not the same thing…
> Best,
> Peter
> >
> > On Mon, May 16, 2016 at 9:45 AM, Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
> > Hello:
> > By using VMD in text mode (psfgen) with CHARMM36, I am getting error in
> MD (NAMD2.11):
> >
> > ERROR: Unable to find angleparams for CC CT1 NH2 (atoms 2971 2974 2980)
> >
> > Actually, ID/atomtype is
> >
> > 2971 NH2
> >
> > 2974 CT1
> >
> > 2980 CC
> >
> > for a CYS ligand made NH2 with PRES NNEU.
> > ------------------
> >
> > In used top_all36_prot.prm, angleparams for
> >
> > NH2 CC CT1
> >
> > NH2 CC CT2
> >
> > NH2 CC CT3
> >
> > do exist.
> > ----------------------
> >
> > Thanks for advice
> >
> > francesco pietra
> >
> >
> >
> > Could the issue arise from having
> >
>
>

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