From: Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (gareth.b.shannon_at_nasa.gov)
Date: Thu May 25 2017 - 10:49:32 CDT
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 29)
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,
Gareth
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