From: Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (gareth.b.shannon_at_nasa.gov)
Date: Thu May 25 2017 - 16:24:08 CDT
Many thanks for your response. You understand though that NN2 and NN2B should not be able to 'see' each other. As one is annihilated the other is appearing. For this reason I don't see why an angle term needs to be specified.
Does this change your point of view?
From: Jeff Comer [jeffcomer_at_gmail.com]
Sent: 25 May 2017 14:16
To: NAMD list; Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION]
Subject: Re: namd-l: Error regarding missing angles between perturbed groups for fep calculation
The error means that the parameter files you are including with
"parameters" keywords in your NAMD configuration file do not include
an angle for the atom types NN2 CN7B NN2B. I'm guessing you are using
"par_all36_na.prm". This parameter may be missing because your FEP
structure has some unusual bonding topology. You either need to change
the topology or determine reasonable values for these parameters.
Jeffrey Comer, PhD
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
On Thu, May 25, 2017 at 10:49 AM, Shannon, Gareth Bayley.
(ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION]
> Hello all,
> I am trying to do FEP to get the delta G of ATP to GTP in solution.
> I am using:
> To build the vacuum psf: PSFGEN 1.5.0 from NAMD 2.8
> To solvate and add ions: VMD 1.9.2
> To perform dynamics: NAMD 2.12
> I am still getting an error due to angles being missing between the two
> perturbed groups which I understand shouldn't be an issue for the NAMD
> version I am using (later than 2.7b2):
> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NN2 CN7B NN2B (ATOMS 10 4
> The two nitrogen atoms referenced (atoms 10 and 29) above are the equivalent
> atoms in the two perturbed groups.
> Can anyone advise how to go about solving this problem please?
> Many thanks,
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