From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Tue May 17 2016 - 09:29:52 CDT
This is a pretty rare case, a single amino acid terminated on both ends, so it’s not surprising that it was overlooked in the parameter file. However, you should be able to easily identify appropriate parameters by analogy.
Best,
JC
> On May 16, 2016, at 9:54 AM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>
> 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 <mailto: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 <mailto: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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