From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Jan 07 2015 - 02:55:16 CST
with namd 2.10 error in trying GBIS minimization of par7/rst7 amber input
Reading parm file (./PROT.parm7) ...
PARM file in AMBER 7 format
Warning: Skipping ATOMIC_NUMBER in parm file while seeking MASS.
Warning: Skipping SCEE_SCALE_FACTOR in parm file while seeking SOLTY.
Warning: Skipping SCNB_SCALE_FACTOR in parm file while seeking SOLTY.
Warning: Encounter 10-12 H-bond term
Warning: Found 919 H-H bonds.
Command = zcat ./PROT.rst7.Z
Filename.Z = ./PROT.rst7.Z
Command = gzip -d -c ./PROT.rst7.gz
Filename.gz = ./PROT.rst7.gz
FATAL ERROR: Can't open AMBER coordinate file!: No such file or directory
# AMBER force field
amber on # expect to read parm7 file
parmfile ./PROT.parm7 #input parm7 file from xleap
ambercoor ./PROT.rst7 # input coordinate file from xleap
Notice that I got minimization of the active center of PROT by using the
same GBIS minimization file layout.
Is "rst7" now confusing the parser?
thanks for advice
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