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
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?
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