VMD-L Mailing List

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Nov 22 2005 - 04:32:02 CST

"auto none" automatically generates angles and dihedrals based on bonds, since the topology file don't list angles and dihedrals. This is specially needed when you apply patches on your protein (such as ACE or CT1) or with water.
 
Hope it is clear,
Michel

________________________________

From: hodak_at_chips.ncsu.edu [mailto:hodak_at_chips.ncsu.edu]
Sent: Tue 11/22/2005 4:16 AM
To: Michel Espinoza-Fonseca
Cc: vmd-l_at_ks.uiuc.edu
Subject: RE: vmd-l: Uncharged terminal ends?

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
> > >
> > >
> >
> >
> >
>
>
>