VMD-L Mailing List

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Nov 22 2005 - 04:18:27 CST

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
> >
> >
>
>
>