Re: parameter file for ACE and CT3 cap

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Mon Sep 03 2018 - 11:59:40 CDT

Thanks Victor
                         Yes the psfgen is working. Some how quick MD was not working. Although the structure was looking ok.

Thanks
Dhiraj

> On Sep 3, 2018, at 11:52 AM, Victor Kwan <vkwan8_at_uwo.ca> wrote:
>
> 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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