From: Tom Caulfield (thomas.caulfield_at_chemistry.gatech.edu)
Date: Thu Jan 27 2005 - 02:29:47 CST
Hello there,
I am trying to get a psf file generated for a tRNA pdb file (which has
some non-standard nucleotides) I have and have tried a plethora of
topology files...but I always get:
>Main< (0 The Simulation) 135 % topology
toppar_all27_na_base_modifications.str
reading topology file toppar_all27_na_base_modifications.str
CHARMM27 All-Hydrogen Nucleic Acid Force Toppar Stream File
Collection of residues and patches for base modifications
A.D. MacKerell, Jr., July 2001
ERROR! Unusual CHARMM version record.
residues and patches associated with base modifications
ERROR! FAILED TO RECOGNIZE 31
duplicate residue key 5MC1 will be ignored
duplicate residue key 5MC2 will be ignored
duplicate residue key INO1 will be ignored
duplicate residue key GUT1 will be ignored
duplicate residue key CYT1 will be ignored
duplicate residue key 1EG will be ignored
duplicate residue key 3EC will be ignored
duplicate residue key CETG will be ignored
duplicate residue key DFT will be ignored
duplicate residue key DFTO will be ignored
duplicate residue key DFB will be ignored
duplicate residue key THYM will be ignored
duplicate residue key THYE will be ignored
ERROR! FAILED TO RECOGNIZE READ
parameters developed in collaboration with Daniel Barsky
ERROR! Failed to parse bond statement.
ERROR! FAILED TO RECOGNIZE CN1
ERROR! FAILED TO RECOGNIZE CN1
ERROR! FAILED TO RECOGNIZE CN1
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE NN1C
ERROR! FAILED TO RECOGNIZE NN2C
ERROR! FAILED TO RECOGNIZE NN2G
ERROR! FAILED TO RECOGNIZE NN3
ERROR! FAILED TO RECOGNIZE CNA
ERROR! FAILED TO RECOGNIZE CN9
ERROR! FAILED TO RECOGNIZE CN8
ERROR! FAILED TO RECOGNIZE CN7B
ERROR! FAILED TO RECOGNIZE HNP
ERROR! FAILED TO RECOGNIZE CNA2
ERROR! FAILED TO RECOGNIZE HN3
ERROR! FAILED TO RECOGNIZE CNA2
ERROR! FAILED TO RECOGNIZE CN3T
ERROR! FAILED TO RECOGNIZE CNE2
ERROR! FAILED TO RECOGNIZE CNE2
ERROR! FAILED TO RECOGNIZE CNE1
ERROR! Failed to parse angle statement.
ERROR! FAILED TO RECOGNIZE CN1
ERROR! FAILED TO RECOGNIZE NN3G
ERROR! FAILED TO RECOGNIZE NN3G
ERROR! FAILED TO RECOGNIZE NN3G
ERROR! FAILED TO RECOGNIZE ON5
ERROR! FAILED TO RECOGNIZE CN1
ERROR! FAILED TO RECOGNIZE NN2C
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE NN2C
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE CN1
ERROR! FAILED TO RECOGNIZE NN2C
ERROR! FAILED TO RECOGNIZE NN2C
ERROR! FAILED TO RECOGNIZE CN3
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE CN1
ERROR! FAILED TO RECOGNIZE NN2G
ERROR! FAILED TO RECOGNIZE NN2G
ERROR! FAILED TO RECOGNIZE CN1
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE CN9
ERROR! FAILED TO RECOGNIZE NN3
ERROR! FAILED TO RECOGNIZE CN8
ERROR! FAILED TO RECOGNIZE NN2G
ERROR! FAILED TO RECOGNIZE CNA
ERROR! FAILED TO RECOGNIZE CNA
ERROR! FAILED TO RECOGNIZE CNA2
ERROR! FAILED TO RECOGNIZE CNA2
ERROR! FAILED TO RECOGNIZE CN7B
ERROR! FAILED TO RECOGNIZE CN7B
ERROR! FAILED TO RECOGNIZE CN9
ERROR! FAILED TO RECOGNIZE CN9
ERROR! FAILED TO RECOGNIZE CN8
ERROR! FAILED TO RECOGNIZE ON6
ERROR! FAILED TO RECOGNIZE HN7
ERROR! FAILED TO RECOGNIZE HN9
ERROR! FAILED TO RECOGNIZE HNP
ERROR! FAILED TO RECOGNIZE HNP
ERROR! FAILED TO RECOGNIZE HN3
ERROR! FAILED TO RECOGNIZE FNA
ERROR! FAILED TO RECOGNIZE CN1
ERROR! FAILED TO RECOGNIZE CN3
ERROR! FAILED TO RECOGNIZE CN3T
ERROR! FAILED TO RECOGNIZE CN3T
ERROR! FAILED TO RECOGNIZE CNE2
ERROR! FAILED TO RECOGNIZE HNE2
ERROR! FAILED TO RECOGNIZE HNE2
ERROR! Failed to parse dihedral statement.
ERROR! FAILED TO RECOGNIZE ON5
ERROR! FAILED TO RECOGNIZE CN5G
ERROR! FAILED TO RECOGNIZE CN1
ERROR! FAILED TO RECOGNIZE NN3G
ERROR! FAILED TO RECOGNIZE NN3G
ERROR! FAILED TO RECOGNIZE NN3G
ERROR! FAILED TO RECOGNIZE NN3G
ERROR! FAILED TO RECOGNIZE CN5G
ERROR! FAILED TO RECOGNIZE HN1
ERROR! FAILED TO RECOGNIZE HN1
ERROR! FAILED TO RECOGNIZE HN1
ERROR! FAILED TO RECOGNIZE NN1C
ERROR! FAILED TO RECOGNIZE CN3
ERROR! FAILED TO RECOGNIZE NN2
ERROR! FAILED TO RECOGNIZE NN2
ERROR! FAILED TO RECOGNIZE HN2
ERROR! FAILED TO RECOGNIZE HN2
ERROR! FAILED TO RECOGNIZE HN2
ERROR! FAILED TO RECOGNIZE ON1C
ERROR! FAILED TO RECOGNIZE CN5G
ERROR! FAILED TO RECOGNIZE ON1
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE CN1
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE CN1
ERROR! FAILED TO RECOGNIZE NN2G
ERROR! FAILED TO RECOGNIZE NN2
ERROR! FAILED TO RECOGNIZE CN8
ERROR! FAILED TO RECOGNIZE CN8
ERROR! FAILED TO RECOGNIZE CN8
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE CN1
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE CN1
ERROR! FAILED TO RECOGNIZE NN3
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE CN1
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE CN1
ERROR! FAILED TO RECOGNIZE NN2G
ERROR! FAILED TO RECOGNIZE NN2G
ERROR! FAILED TO RECOGNIZE NN3
ERROR! FAILED TO RECOGNIZE CNA
ERROR! FAILED TO RECOGNIZE CNA2
ERROR! FAILED TO RECOGNIZE CNA2
ERROR! FAILED TO RECOGNIZE CNA
ERROR! FAILED TO RECOGNIZE CNA
ERROR! FAILED TO RECOGNIZE HN7
ERROR! FAILED TO RECOGNIZE HN8
ERROR! FAILED TO RECOGNIZE HN7
ERROR! FAILED TO RECOGNIZE HN9
ERROR! FAILED TO RECOGNIZE HN9
ERROR! FAILED TO RECOGNIZE CN7
ERROR! FAILED TO RECOGNIZE CN8
ERROR! FAILED TO RECOGNIZE CN8
ERROR! FAILED TO RECOGNIZE CN7B
ERROR! FAILED TO RECOGNIZE CN7B
ERROR! FAILED TO RECOGNIZE CN9
ERROR! FAILED TO RECOGNIZE CN9
ERROR! FAILED TO RECOGNIZE HN7
ERROR! FAILED TO RECOGNIZE HNP
ERROR! FAILED TO RECOGNIZE HNP
ERROR! FAILED TO RECOGNIZE HN3
ERROR! FAILED TO RECOGNIZE HNP
ERROR! FAILED TO RECOGNIZE HNP
ERROR! FAILED TO RECOGNIZE HNP
ERROR! FAILED TO RECOGNIZE HNP
ERROR! FAILED TO RECOGNIZE HNP
ERROR! FAILED TO RECOGNIZE HN3
ERROR! FAILED TO RECOGNIZE FNA
ERROR! FAILED TO RECOGNIZE FNA
ERROR! FAILED TO RECOGNIZE FNA
ERROR! FAILED TO RECOGNIZE FNA
ERROR! FAILED TO RECOGNIZE ON6
ERROR! FAILED TO RECOGNIZE ON6
ERROR! FAILED TO RECOGNIZE CN7
ERROR! FAILED TO RECOGNIZE CN7
ERROR! FAILED TO RECOGNIZE ON1
ERROR! FAILED TO RECOGNIZE HN3
ERROR! FAILED TO RECOGNIZE CN1
ERROR! FAILED TO RECOGNIZE CN3
ERROR! FAILED TO RECOGNIZE CNE2
ERROR! FAILED TO RECOGNIZE CNE2
ERROR! FAILED TO RECOGNIZE CNE2
ERROR! FAILED TO RECOGNIZE CNE2
ERROR! FAILED TO RECOGNIZE HNE2
ERROR! FAILED TO RECOGNIZE HNE2
ERROR! Failed to parse improper statement.
ERROR! FAILED TO RECOGNIZE CN1
ERROR! FAILED TO RECOGNIZE CN2
ERROR! FAILED TO RECOGNIZE RETURN
or if I use:
127 % topology par_all27_na.prn
I get
RROR! FAILED TO RECOGNIZE CN5
ERROR! FAILED TO RECOGNIZE CN5G
ERROR! FAILED TO RECOGNIZE CN7
ERROR! FAILED TO RECOGNIZE CN7B
ERROR! FAILED TO RECOGNIZE CN7C
ERROR! FAILED TO RECOGNIZE CN7D
ERROR! FAILED TO RECOGNIZE CN8
ERROR! FAILED TO RECOGNIZE CN8B
ERROR! FAILED TO RECOGNIZE CN9
ERROR! FAILED TO RECOGNIZE CNE1
ERROR! FAILED TO RECOGNIZE CNE2
ERROR! FAILED TO RECOGNIZE CNA
ERROR! FAILED TO RECOGNIZE CNA2
ERROR! FAILED TO RECOGNIZE CN6
ERROR! FAILED TO RECOGNIZE CN7E
ERROR! FAILED TO RECOGNIZE FN1
ERROR! FAILED TO RECOGNIZE FNA
ERROR! FAILED TO RECOGNIZE P
ERROR! FAILED TO RECOGNIZE P2
ERROR! FAILED TO RECOGNIZE P3
ERROR! FAILED TO RECOGNIZE CPH1
ERROR! FAILED TO RECOGNIZE CPH2
ERROR! FAILED TO RECOGNIZE NR1
ERROR! FAILED TO RECOGNIZE NR2
ERROR! FAILED TO RECOGNIZE HR3
ERROR! FAILED TO RECOGNIZE HR1
ERROR! FAILED TO RECOGNIZE SOD
ERROR! FAILED TO RECOGNIZE POT
ERROR! FAILED TO RECOGNIZE CLA
ERROR! FAILED TO RECOGNIZE CAL
ERROR! FAILED TO RECOGNIZE MG
ERROR! FAILED TO RECOGNIZE CES
ERROR! FAILED TO RECOGNIZE ZN
ERROR! FAILED TO RECOGNIZE DUM
ERROR! FAILED TO RECOGNIZE NBFIX
ERROR! FAILED TO RECOGNIZE HBOND
I must have my approach all wrong...I was able to do a protein
fine...what do I need to get the RNA (tRNA) working? I realize I will
need to ionize it explicitly after this to get the ionization in check
too.
Thanks so much,
-Tom
***************************************
Tom Caulfield, Ph. D. Student
School of Chemistry & Biochemistry
Cherry Emerson Bldg., RM 329
GeorgiaInstitute
ofTechnology
Atlanta, GA 30332-0400
***************************************
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