From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri Jan 21 2011 - 11:01:56 CST
Your topology contains duplicate bonds, including N-CA: that is why
extraneous angles get generated. For clarity, you can also remove all
DONOR, ACCEPTOR, and DOUBLE entries (all of them deprecated), as well
as the explicit ANGLE and DIHEDRAL declarations.
On 21 January 2011 13:44, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
> 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?
> 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
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