From: Pardis Tabaee (pardis.tabaee.d_at_hotmail.co.uk)
Date: Fri May 20 2016 - 11:12:24 CDT
Are you sure about this? Because your ligand is a cysteine, right?
Are the par files and top files of the same edition? par_all36... and top_all36, or are they different? Because some of the atom type "labels" have changed throughout the years. E.g. in 22 NH2 was an amidic NH2. I don't think the angle will be missing if your ligand is cysteine, I think it's somewhere, but maybe the atom type may be wrong?
Good luck, either case.
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Francesco Pietra <chiendarret_at_gmail.com>
Sent: 16 May 2016 14:54
To: Peter Freddolino
Cc: NAMD; VMD Mailing List
Subject: namd-l: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params
yes, I made that clear. Apparently, to my disappointment, NNEU was not accompanied by appropriate parameters for atom C being terminal.
all the best
On Mon, May 16, 2016 at 2:46 PM, Peter Freddolino <petefred_at_umich.edu<mailto:petefred_at_umich.edu>> wrote:
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...
> On Mon, May 16, 2016 at 9:45 AM, Francesco Pietra <chiendarret_at_gmail.com<mailto:chiendarret_at_gmail.com>> wrote:
> 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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