From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Aug 29 2012 - 13:05:15 CDT
Dear NAMD/VMD users,
I am trying to prepare a molecule for FEP calculation. I am using vmd to
prepare the psf file and namd for the simulation. Whole process is smooth,
since the hybrid topology file is available in VMD directory. However, when
I am running NAMD simulation, I am getting the error message.
Reason: FATAL ERROR: UNABLE TO FIND CROSSTERM PARAMETERS FOR C NH1 CT1
C NH1 CT1 C NH1
The error is obvious because the hybrid parameter file is missing. I have
regular par_all22_prot.inp *parameter file* and *hybrid topology* file
top_all27_hybrid.inp. Mutation from Tyr to Ala is easy using* **hybrid
topology* file but to run the simulation I need *hybrid parameter* file. I
already used the alchemify plugin in VMD to correct the psf file.
However, using both psf file, I am getting the same error message.
Does any one know where i can find the *hybrid parameter* file for all
amino acids used in FEP NAMD simulation.
I will highly appreciate your help.
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