VMD-L Mailing List

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Nov 22 2005 - 03:57:06 CST

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
>
>