Failure MD with par7/rst7 amber input

From: Francesco Pietra (
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

min-01.conf contains:

# 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

francesco pietra

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