From: Spiro Pavlopoulos (s.pavlopoulos_at_uconn.edu)
Date: Tue Aug 21 2007 - 15:02:39 CDT
I am looking to do dynamics on peptides with phophorylated serines and am
just trying to get to the point where I can run a minimization. After
looking through the list I have succesfully used psfgen to construct the pdb
and psf files by using top_all27_prot_na.rtf and toppar_prot_na_all.str .
However when I try to run a simple minimization with NAMD using
par_all27_prot_na.prm, it returns the following error.
FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND CT2 - ON2 IN PARAMETER
FILES
This is the bond between the CB of the serine sidechain and the oxygen of
the phosphate group which apparently is not parameterized in
par_all27_prot_na.prm
If I have understood correctly from messages on the list, the stream file
contains these parameters but I do not know how to make NAMD read these
parameters from .str.
I have tried adding the line
parameters /toppar/stream/toppar_prot_na_all.str
to the namd input file but it returns a message saying it cannot read
the file.
I would rather avoid cutting and pasting parameters from the .str to the
.prm file. If someone could let me know the correct procedure or whether I
am way off base I would greatly appreciate it.
With Thanks
Spiro
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