From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Sun Jan 27 2013 - 16:06:20 CST
Hi all,
I am using NAMD to simulate a protein complex - I have generate the
parameters using ambertool1.5 and in the logfile a total 475 impropers
are generated. When I start my minimization and equilibration using
NAMD I get the following output
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : ALL
Info: ERROR TOLERANCE : 0.0005
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED 1359317928
Info: USE HYDROGEN BONDS? NO
Info: Using AMBER format force field!
Info: AMBER PARM FILE dadp_solv.prmtop
Info: AMBER COORDINATE FILE dadp_solv.inpcrd
Info: Exclusions will be read from PARM file!
Info: SCNB (VDW SCALING) 2
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES min8.restart.coor
Reading parm file (dadp_solv.prmtop) ...
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 5990 H-H bonds.
Info: SUMMARY OF PARAMETERS:
Info: 80 BONDS
Info: 182 ANGLES
Info: 182 HARMONIC
Info: 0 COSINE-BASED
Info: 251 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 0 VDW
Info: 253 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PDB FILE: 1.90735e-06
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 20156 ATOMS
Info: 20173 BONDS
Info: 3963 ANGLES
Info: 9847 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
which states that no improper angles are read, which I can also
confirm looking at the output where hydrogens from ASN or ARG are not
planar. I have set the following flag for amber in the configuration
file
amber on # Specify this is AMBER force field
parmfile solv1.prmtop # Input PARM file
ambercoor solv1.inpcrd # Input coordinate file
how to fix this or is it an amber issue? Thanks for any help
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