VMD-L Mailing List

From: hodak_at_chips.ncsu.edu
Date: Tue Nov 22 2005 - 04:16:55 CST

With this I am namd simulation will start. Now what is does "auto none"
actually do?

Thanks,
        Miro

On Tue, 22 Nov 2005, Michel Espinoza-Fonseca wrote:

> mmmm... try to rebuild your system using
>
> first ACE
> last CT1
> auto none
>
> and then see if it works...
>
> ________________________________
>
> From: hodak_at_chips.ncsu.edu [mailto:hodak_at_chips.ncsu.edu]
> Sent: Tue 11/22/2005 4:00 AM
> To: Michel Espinoza-Fonseca
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: RE: vmd-l: Uncharged terminal ends?
>
>
>
> I cannot minimize the system (at least not with namd), since I get that error
> about HB CT1 HB angle parameters when I try to run namd with my system.
>
> On Tue, 22 Nov 2005, Michel Espinoza-Fonseca wrote:
>
> > That's weird... Are you minimizing your system first ? Usually I get the same thing you described (multiple bonds on the ACE or NME terminals), but you can easily solve this problem by subjecting your system to a short (~1000 steps) minimization.
> >
> > After that you should't have any problem.
> >
> > Hope it helps.
> >
> > Michel
> >
> > ________________________________
> >
> > From: owner-vmd-l_at_ks.uiuc.edu on behalf of hodak_at_chips.ncsu.edu
> > Sent: Tue 11/22/2005 3:18 AM
> > To: Justin Gullingsrud
> > Cc: vmd-l_at_ks.uiuc.edu
> > Subject: Re: vmd-l: Uncharged terminal ends?
> >
> >
> >
> > This helped a lot. I decided that I want acetylated N-terminus and
> > methylated C-terminus. Using
> >
> > first ACE
> > last CT1
> >
> > I can get the ends I want, although vmd shows extra bonds that those added
> > groups have carbons connected to N or C. I am not sure if this is a
> > problem or not.
> > I went ahead and used generated psf and pdb files as input for namd
> > simulation, but I get the following error:
> >
> > FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB CT1 HB
> > ------------- Processor 0 Exiting: Called CmiAbort ------------
> > Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB CT1 HB
> >
> > Charm++ fatal error:
> > FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB CT1 HB
> >
> > The problem seems to be the C-terminal end, omitting "last CT1" namd
> > simulation runs without problems.
> >
> > Any idea what the problem is and how it can be solved?
> >
> > Thanks,
> > Miro
> >
> >
> >
> >
> > On Mon, 21 Nov 2005, Justin Gullingsrud wrote:
> >
> > > Hi,
> > >
> > > You probably want an acetylated N terminus, then, which you can get by
> > > specifying "first ACE". I'm not sure what kind of C terminus you're
> > > looking for, but check out the PRES patches in the topology file to
> > > see what's available.
> > >
> > > Hope this helps,
> > > Justin
> > >
> > >
> >
> >
> >
>
>
>