Re: parameter file for ACE and CT3 cap

From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Mon Sep 03 2018 - 11:52:35 CDT

Hi Dhiraj,

Chances are you did not cap (ie. patch the c-terminus) the protein
properly. Try using psfgen instead of QwikMD.

Rgds,

Victor

On 09/02/2018 08:45 PM, Dhiraj Srivastava wrote:
> Hi all
>         I am trying to simulate protein complex fragment where I want
> to cap N terminus of one protein and C terminus of other to avoid
> non-physiological interaction. However NAMD is complaining about
> FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C OC (ATOMS 7194 7203)
>
> which parameter file do I need to use for ACE and CT3 capping? I used
> QuickMD to generate the files.
>
> Thank you
> Dhiraj

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