Re: parameter file for ACE and CT3 cap

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Tue Sep 04 2018 - 08:02:57 CDT

Dear Dhiraj,

I am glad that your simulation is working properly now. Would it be
possible for you to say what version of QwikMD were you using? Does the
same behavior happen when you use the beta version deposited in the website
(https://www.ks.uiuc.edu/Research/qwikmd/)? If that is the case, would you
mind to send me (off the mailing list) the structure and instructions how
you are preparing so I can fix QwikMD/Autopsf?

As additional information, QwikMD uses NTER (GLYP and PROP in the case of
terminal Glycine and Proline), CTER terminus patches automatically. I have
on my TODO list to give the user the option to chose the patch, but it is
not yet implemented.

Best

João

On Mon, Sep 3, 2018 at 12:01 PM Dhiraj Srivastava <dhirajks_at_gmail.com>
wrote:

> 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
> >
>
>

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851

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