RE: Missing angle parameters NH1 CT1 NH1

From: Christian Jorgensen (christian.jorgensen_at_merton.ox.ac.uk)
Date: Fri Jan 21 2011 - 12:01:09 CST

Thanks again,

however, I still think there is a mistake in my topology file

ERROR: Atom 30713 velocity is -10774.3 -15343.8 13.7328 (limit is 6000)
ERROR: Atom 30714 velocity is 8091.21 11521.1 -18.2863 (limit is 6000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 30710 velocity is -6387.76 -16834.9 -6212.12 (limit is 6000)
ERROR: Atom 30711 velocity is 4798.22 12633.7 4668.04 (limit is 6000)
ERROR: Atom 30718 velocity is -6388.21 -16829.8 -6213.13 (limit is 6000)
ERROR: Atom 30719 velocity is 4790.47 12633 4662.15 (limit is 6000)
ERROR: Atoms moving too fast; simulation has become unstable.

This corresponds to
ATOM 30710 CM2 MUT U 71 -13.636 -3.061 10.245 1.00 0.00 U1 C
ATOM 30711 OM1 MUT U 71 -13.227 -1.983 10.643 1.00 0.00 U1 O
ATOM 30713 C MUT U 71 -12.339 -3.219 6.007 1.00 0.00 U1 C
ATOM 30714 O MUT U 71 -11.625 -2.202 6.006 1.00 0.00 U1 O
ATOM 30718 CD MUT U 71 -13.636 -3.061 10.245 1.00 0.00 U1 C
ATOM 30719 OE1 MUT U 71 -13.227 -1.983 10.643 1.00 0.00 U1 O

This problem suggests that these atoms are clashing and overlapping, which they of course are (it is a mutated pdb file after all).
However, I have amended the psf file with Alchemify to create exclusion pairs that should prevent this from happening.

Any ideas on what I could do?

Thanks
Christian
________________________________________
From: heninj_at_gmail.com [heninj_at_gmail.com] On Behalf Of Jérôme Hénin [jhenin_at_ifr88.cnrs-mrs.fr]
Sent: Friday, January 21, 2011 12:44 PM
To: Christian Jorgensen
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Missing angle parameters NH1 CT1 NH1

Hi Christian,

Besides a few unnecessary lines, nothing strikes me as wrong in the
topology. Can you send me (off-list) your PSF and PDB files?

Jerome

On 21 January 2011 11:39, Christian Jorgensen
<christian.jorgensen_at_merton.ox.ac.uk> wrote:
> Hi all,
> I am trying to construct a mutated topology file for a GluP to Glu free energy alchemical transformation using NAMD
> The error I keep getting is that a non-existent angle NH1 - CT1 - NH1 (i.e. N - CA - N) is missing in the parameter file:
>
> FATAL ERROR: Unable to find angle parameters for NH1 CT1 NH1
>
> This suggests that in my topology file there is a mistake, i.e. I must be telling NAMD that the bonds N-CA-N exist (which is false)
> and that there should logically exist an angle parameter for these bonds.
>
>
>
> My topology file is: http://peecee.dk/upload/view/285554
>
> I would appreciate any help out there
>
> Thanks,
> Christian
>
>

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